diff --git a/hadoop-tools/hadoop-azure/src/main/java/org/apache/hadoop/fs/azure/AzureNativeFileSystemStore.java b/hadoop-tools/hadoop-azure/src/main/java/org/apache/hadoop/fs/azure/AzureNativeFileSystemStore.java
index 7463bc30ea9..cb3e9f65188 100644
--- a/hadoop-tools/hadoop-azure/src/main/java/org/apache/hadoop/fs/azure/AzureNativeFileSystemStore.java
+++ b/hadoop-tools/hadoop-azure/src/main/java/org/apache/hadoop/fs/azure/AzureNativeFileSystemStore.java
@@ -450,7 +450,9 @@ public class AzureNativeFileSystemStore implements NativeFileSystemStore {
       // Add to this the hbase root directory, or /hbase is that is not set.
       hbaseRoot = verifyAndConvertToStandardFormat(
           sessionConfiguration.get("hbase.rootdir", "hbase"));
-      atomicRenameDirs.add(hbaseRoot);
+      if (hbaseRoot != null) {
+        atomicRenameDirs.add(hbaseRoot);
+      }
     } catch (URISyntaxException e) {
       LOG.warn("Unable to initialize HBase root as an atomic rename directory.");
     }
diff --git a/hadoop-tools/hadoop-azure/src/test/java/org/apache/hadoop/fs/azure/TestNativeAzureFileSystemAtomicRenameDirList.java b/hadoop-tools/hadoop-azure/src/test/java/org/apache/hadoop/fs/azure/TestNativeAzureFileSystemAtomicRenameDirList.java
new file mode 100644
index 00000000000..b9cca25c6f6
--- /dev/null
+++ b/hadoop-tools/hadoop-azure/src/test/java/org/apache/hadoop/fs/azure/TestNativeAzureFileSystemAtomicRenameDirList.java
@@ -0,0 +1,49 @@
+/**
+ * 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.fs.azure;
+
+import java.io.IOException;
+import java.net.URI;
+
+import org.apache.hadoop.conf.Configuration;
+import org.junit.Test;
+
+public class TestNativeAzureFileSystemAtomicRenameDirList extends NativeAzureFileSystemBaseTest {
+  private AzureBlobStorageTestAccount testAccount;
+
+  // HBase-site config controlling HBase root dir
+  private static final String HBASE_ROOT_DIR_CONF_STRING = "hbase.rootdir";
+  private static final String HBASE_ROOT_DIR_VALUE_ON_DIFFERENT_FS = "wasb://somedifferentfilesystem.blob.core.windows.net/hbase";
+  @Override
+  protected AzureBlobStorageTestAccount createTestAccount() throws Exception {
+    testAccount = AzureBlobStorageTestAccount.create();
+    return testAccount;
+  }
+
+  @Test
+  public void testAzureNativeStoreIsAtomicRenameKeyDoesNotThrowNPEOnInitializingWithNonDefaultURI () throws IOException {
+    NativeAzureFileSystem azureFs = (NativeAzureFileSystem)fs;
+    AzureNativeFileSystemStore azureStore = azureFs.getStore();
+    Configuration conf = fs.getConf();
+    conf.set(HBASE_ROOT_DIR_CONF_STRING, HBASE_ROOT_DIR_VALUE_ON_DIFFERENT_FS);
+    URI uri = fs.getUri();
+    fs.initialize(uri, conf);
+    azureStore.isAtomicRenameKey("anyrandomkey");
+  }
+}