diff --git a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/LeveldbConfigurationStore.java b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/LeveldbConfigurationStore.java
index bcdfb5924de..b43bcb839c0 100644
--- a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/LeveldbConfigurationStore.java
+++ b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/LeveldbConfigurationStore.java
@@ -344,11 +344,15 @@ public class LeveldbConfigurationStore extends YarnConfigurationStore {
 
   @Override
   public void storeVersion() throws Exception {
-    String key = VERSION_KEY;
-    byte[] data = ((VersionPBImpl) CURRENT_VERSION_INFO).getProto()
+    storeVersion(CURRENT_VERSION_INFO);
+  }
+
+  @VisibleForTesting
+  protected void storeVersion(Version version) throws Exception {
+    byte[] data = ((VersionPBImpl) version).getProto()
         .toByteArray();
     try {
-      db.put(bytes(key), data);
+      db.put(bytes(VERSION_KEY), data);
     } catch (DBException e) {
       throw new IOException(e);
     }
diff --git a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfStoreVersionIncompatibleException.java b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfStoreVersionIncompatibleException.java
new file mode 100644
index 00000000000..2213ee24c6e
--- /dev/null
+++ b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfStoreVersionIncompatibleException.java
@@ -0,0 +1,43 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.hadoop.yarn.server.resourcemanager.scheduler.capacity.conf;
+
+import org.apache.hadoop.yarn.exceptions.YarnException;
+
+/**
+ * This exception is thrown by {@link YarnConfigurationStore} if it's loading
+ * an incompatible persisted schema version.
+ */
+public class YarnConfStoreVersionIncompatibleException extends
+    YarnException {
+  private static final long serialVersionUID = -2829858253579013629L;
+
+  public YarnConfStoreVersionIncompatibleException(Throwable cause) {
+    super(cause);
+  }
+
+  public YarnConfStoreVersionIncompatibleException(String message) {
+    super(message);
+  }
+
+  public YarnConfStoreVersionIncompatibleException(
+      String message, Throwable cause) {
+    super(message, cause);
+  }
+}
diff --git a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfigurationStore.java b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfigurationStore.java
index 34aa17428c2..e8e3ecf87c8 100644
--- a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfigurationStore.java
+++ b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/main/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/YarnConfigurationStore.java
@@ -23,7 +23,6 @@ import org.slf4j.LoggerFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.yarn.server.records.Version;
 import org.apache.hadoop.yarn.server.resourcemanager.RMContext;
-import org.apache.hadoop.yarn.server.resourcemanager.recovery.RMStateVersionIncompatibleException;
 import org.apache.hadoop.yarn.server.resourcemanager.scheduler.capacity.CapacityScheduler;
 
 import java.io.IOException;
@@ -103,6 +102,7 @@ public abstract class YarnConfigurationStore {
 
   /**
    * Logs the configuration change to backing store.
+   *
    * @param logMutation configuration change to be persisted in write ahead log
    * @throws IOException if logging fails
    */
@@ -169,23 +169,22 @@ public abstract class YarnConfigurationStore {
   protected abstract Version getCurrentVersion();
 
   public void checkVersion() throws Exception {
-    // TODO this was taken from RMStateStore. Should probably refactor
     Version loadedVersion = getConfStoreVersion();
-    LOG.info("Loaded configuration store version info " + loadedVersion);
-    if (loadedVersion != null && loadedVersion.equals(getCurrentVersion())) {
+    Version currentVersion = getCurrentVersion();
+    LOG.info("Loaded configuration store version info {}", loadedVersion);
+
+    // when hard-coded schema version (currentVersion) is null the version check
+    // is unnecessary
+    if (currentVersion == null || currentVersion.equals(loadedVersion)) {
       return;
     }
     // if there is no version info, treat it as CURRENT_VERSION_INFO;
-    if (loadedVersion == null) {
-      loadedVersion = getCurrentVersion();
-    }
-    if (loadedVersion.isCompatibleTo(getCurrentVersion())) {
-      LOG.info("Storing configuration store version info "
-          + getCurrentVersion());
+    if (loadedVersion == null || loadedVersion.isCompatibleTo(currentVersion)) {
+      LOG.info("Storing configuration store version info {}", currentVersion);
       storeVersion();
     } else {
-      throw new RMStateVersionIncompatibleException(
-          "Expecting configuration store version " + getCurrentVersion()
+      throw new YarnConfStoreVersionIncompatibleException(
+          "Expecting configuration store version " + currentVersion
               + ", but loading version " + loadedVersion);
     }
   }
diff --git a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestInMemoryConfigurationStore.java b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestInMemoryConfigurationStore.java
index c40d16a27cb..5ebad50fe62 100644
--- a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestInMemoryConfigurationStore.java
+++ b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestInMemoryConfigurationStore.java
@@ -18,6 +18,10 @@
 
 package org.apache.hadoop.yarn.server.resourcemanager.scheduler.capacity.conf;
 
+import org.junit.Test;
+
+import static org.junit.Assert.fail;
+
 /**
  * Tests {@link InMemoryConfigurationStore}.
  */
@@ -27,4 +31,13 @@ public class TestInMemoryConfigurationStore extends ConfigurationStoreBaseTest {
   protected YarnConfigurationStore createConfStore() {
     return new InMemoryConfigurationStore();
   }
+
+  @Test
+  public void checkVersion() {
+    try {
+      confStore.checkVersion();
+    } catch (Exception e) {
+      fail("checkVersion threw exception");
+    }
+  }
 }
diff --git a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestLeveldbConfigurationStore.java b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestLeveldbConfigurationStore.java
index 0ae7624d78c..785a910d781 100644
--- a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestLeveldbConfigurationStore.java
+++ b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestLeveldbConfigurationStore.java
@@ -18,6 +18,7 @@
 
 package org.apache.hadoop.yarn.server.resourcemanager.scheduler.capacity.conf;
 
+import org.apache.hadoop.yarn.server.records.Version;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.apache.hadoop.fs.FileUtil;
@@ -78,6 +79,23 @@ public class TestLeveldbConfigurationStore extends ConfigurationStoreBaseTest {
     confStore.close();
   }
 
+  @Test(expected = YarnConfStoreVersionIncompatibleException.class)
+  public void testIncompatibleVersion() throws Exception {
+    try {
+      confStore.initialize(conf, schedConf, rmContext);
+
+      Version otherVersion = Version.newInstance(1, 1);
+      ((LeveldbConfigurationStore) confStore).storeVersion(otherVersion);
+
+      assertEquals("The configuration store should have stored the new" +
+              "version.", otherVersion,
+          confStore.getConfStoreVersion());
+      confStore.checkVersion();
+    } finally {
+      confStore.close();
+    }
+  }
+
   @Test
   public void testPersistConfiguration() throws Exception {
     schedConf.set("key", "val");
diff --git a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestZKConfigurationStore.java b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestZKConfigurationStore.java
index e67e382f71e..6715a0508fa 100644
--- a/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestZKConfigurationStore.java
+++ b/hadoop-yarn-project/hadoop-yarn/hadoop-yarn-server/hadoop-yarn-server-resourcemanager/src/test/java/org/apache/hadoop/yarn/server/resourcemanager/scheduler/capacity/conf/TestZKConfigurationStore.java
@@ -19,6 +19,10 @@
 package org.apache.hadoop.yarn.server.resourcemanager.scheduler.capacity.conf;
 
 import org.apache.hadoop.util.curator.ZKCuratorManager;
+import org.apache.hadoop.yarn.server.records.Version;
+import org.apache.hadoop.yarn.server.records.impl.pb.VersionPBImpl;
+import org.apache.zookeeper.CreateMode;
+import org.apache.zookeeper.data.ACL;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.apache.curator.framework.CuratorFramework;
@@ -49,6 +53,7 @@ import java.io.IOException;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.LinkedList;
+import java.util.List;
 import java.util.Map;
 
 import static org.junit.Assert.assertEquals;
@@ -113,6 +118,29 @@ public class TestZKConfigurationStore extends ConfigurationStoreBaseTest {
         confStore.getConfStoreVersion());
   }
 
+  @Test(expected = YarnConfStoreVersionIncompatibleException.class)
+  public void testIncompatibleVersion() throws Exception {
+    confStore.initialize(conf, schedConf, rmContext);
+
+    Version otherVersion = Version.newInstance(1, 1);
+    String znodeParentPath = conf.get(YarnConfiguration.
+            RM_SCHEDCONF_STORE_ZK_PARENT_PATH,
+        YarnConfiguration.DEFAULT_RM_SCHEDCONF_STORE_ZK_PARENT_PATH);
+    String zkVersionPath = ZKCuratorManager.getNodePath(znodeParentPath,
+        "VERSION");
+    String fencingNodePath = ZKCuratorManager.getNodePath(znodeParentPath,
+        "FENCING");
+    byte[] versionData =
+        ((VersionPBImpl) otherVersion).getProto().toByteArray();
+    List<ACL> zkAcl = ZKCuratorManager.getZKAcls(conf);
+    ((ZKConfigurationStore) confStore).zkManager.safeCreate(zkVersionPath,
+        versionData, zkAcl, CreateMode.PERSISTENT, zkAcl, fencingNodePath);
+
+    assertEquals("The configuration store should have stored the new" +
+        "version.", otherVersion, confStore.getConfStoreVersion());
+    confStore.checkVersion();
+  }
+
   @Test
   public void testPersistConfiguration() throws Exception {
     schedConf.set("key", "val");