diff --git a/server/src/main/java/io/druid/metadata/IndexerSQLMetadataStorageCoordinator.java b/server/src/main/java/io/druid/metadata/IndexerSQLMetadataStorageCoordinator.java
index 2235916a105..03675a28aa5 100644
--- a/server/src/main/java/io/druid/metadata/IndexerSQLMetadataStorageCoordinator.java
+++ b/server/src/main/java/io/druid/metadata/IndexerSQLMetadataStorageCoordinator.java
@@ -29,8 +29,11 @@ import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Ordering;
 import com.google.common.collect.Sets;
+import com.google.common.hash.Hashing;
+import com.google.common.io.BaseEncoding;
 import com.google.inject.Inject;
 import com.metamx.common.IAE;
+import com.metamx.common.StringUtils;
 import com.metamx.common.lifecycle.LifecycleStart;
 import com.metamx.common.logger.Logger;
 import io.druid.indexing.overlord.IndexerMetadataStorageCoordinator;
@@ -447,10 +450,23 @@ public class IndexerSQLMetadataStorageCoordinator implements IndexerMetadataStor
             // Avoiding ON DUPLICATE KEY since it's not portable.
             // Avoiding try/catch since it may cause inadvertent transaction-splitting.
 
+            // UNIQUE key for the row, ensuring sequences do not fork in two directions.
+            // Using a single column instead of (sequence_name, sequence_prev_id) as some MySQL storage engines
+            // have difficulty with large unique keys (see https://github.com/druid-io/druid/issues/2319)
+            final String sequenceNamePrevIdSha1 = BaseEncoding.base16().encode(
+                Hashing.sha1()
+                       .newHasher()
+                       .putBytes(StringUtils.toUtf8(sequenceName))
+                       .putByte((byte) 0xff)
+                       .putBytes(StringUtils.toUtf8(previousSegmentIdNotNull))
+                       .hash()
+                       .asBytes()
+            );
+
             handle.createStatement(
                 String.format(
-                    "INSERT INTO %s (id, dataSource, created_date, start, \"end\", sequence_name, sequence_prev_id, payload) "
-                    + "VALUES (:id, :dataSource, :created_date, :start, :end, :sequence_name, :sequence_prev_id, :payload)",
+                    "INSERT INTO %s (id, dataSource, created_date, start, \"end\", sequence_name, sequence_prev_id, sequence_name_prev_id_sha1, payload) "
+                    + "VALUES (:id, :dataSource, :created_date, :start, :end, :sequence_name, :sequence_prev_id, :sequence_name_prev_id_sha1, :payload)",
                     dbTables.getPendingSegmentsTable()
                 )
             )
@@ -461,6 +477,7 @@ public class IndexerSQLMetadataStorageCoordinator implements IndexerMetadataStor
                   .bind("end", interval.getEnd().toString())
                   .bind("sequence_name", sequenceName)
                   .bind("sequence_prev_id", previousSegmentIdNotNull)
+                  .bind("sequence_name_prev_id_sha1", sequenceNamePrevIdSha1)
                   .bind("payload", jsonMapper.writeValueAsBytes(newIdentifier))
                   .execute();
 
diff --git a/server/src/main/java/io/druid/metadata/SQLMetadataConnector.java b/server/src/main/java/io/druid/metadata/SQLMetadataConnector.java
index 3846298ba3f..a004e69927c 100644
--- a/server/src/main/java/io/druid/metadata/SQLMetadataConnector.java
+++ b/server/src/main/java/io/druid/metadata/SQLMetadataConnector.java
@@ -197,9 +197,10 @@ public abstract class SQLMetadataConnector implements MetadataStorageConnector
                 + "  \"end\" VARCHAR(255) NOT NULL,\n"
                 + "  sequence_name VARCHAR(255) NOT NULL,\n"
                 + "  sequence_prev_id VARCHAR(255) NOT NULL,\n"
+                + "  sequence_name_prev_id_sha1 VARCHAR(255) NOT NULL,\n"
                 + "  payload %2$s NOT NULL,\n"
                 + "  PRIMARY KEY (id),\n"
-                + "  UNIQUE (sequence_name, sequence_prev_id)\n"
+                + "  UNIQUE (sequence_name_prev_id_sha1)\n"
                 + ")",
                 tableName, getPayloadType()
             )