diff --git a/core/src/main/java/org/elasticsearch/index/shard/StoreRecovery.java b/core/src/main/java/org/elasticsearch/index/shard/StoreRecovery.java
index 9216075e822..cfa2ff3dc28 100644
--- a/core/src/main/java/org/elasticsearch/index/shard/StoreRecovery.java
+++ b/core/src/main/java/org/elasticsearch/index/shard/StoreRecovery.java
@@ -436,6 +436,8 @@ final class StoreRecovery {
             final IndexId indexId = repository.getRepositoryData().resolveIndexId(indexName);
             repository.restoreShard(indexShard, restoreSource.snapshot().getSnapshotId(), restoreSource.version(), indexId, snapshotShardId, indexShard.recoveryState());
             indexShard.skipTranslogRecovery();
+            assert indexShard.shardRouting.primary() : "only primary shards can recover from store";
+            indexShard.getEngine().fillSeqNoGaps(indexShard.getPrimaryTerm());
             indexShard.finalizeRecovery();
             indexShard.postRecovery("restore done");
         } catch (Exception e) {
diff --git a/core/src/test/java/org/elasticsearch/snapshots/SharedClusterSnapshotRestoreIT.java b/core/src/test/java/org/elasticsearch/snapshots/SharedClusterSnapshotRestoreIT.java
index 45ec0746a9b..7d6bf0ff912 100644
--- a/core/src/test/java/org/elasticsearch/snapshots/SharedClusterSnapshotRestoreIT.java
+++ b/core/src/test/java/org/elasticsearch/snapshots/SharedClusterSnapshotRestoreIT.java
@@ -36,6 +36,7 @@ import org.elasticsearch.action.admin.cluster.state.ClusterStateResponse;
 import org.elasticsearch.action.admin.cluster.storedscripts.GetStoredScriptResponse;
 import org.elasticsearch.action.admin.indices.flush.FlushResponse;
 import org.elasticsearch.action.admin.indices.settings.get.GetSettingsResponse;
+import org.elasticsearch.action.admin.indices.stats.IndicesStatsResponse;
 import org.elasticsearch.action.admin.indices.stats.ShardStats;
 import org.elasticsearch.action.admin.indices.template.get.GetIndexTemplatesResponse;
 import org.elasticsearch.action.index.IndexRequestBuilder;
@@ -71,8 +72,10 @@ import org.elasticsearch.common.unit.ByteSizeUnit;
 import org.elasticsearch.common.unit.TimeValue;
 import org.elasticsearch.common.xcontent.XContentFactory;
 import org.elasticsearch.common.xcontent.XContentType;
+import org.elasticsearch.index.Index;
 import org.elasticsearch.index.IndexService;
 import org.elasticsearch.index.engine.Engine;
+import org.elasticsearch.index.shard.IndexShard;
 import org.elasticsearch.index.shard.ShardId;
 import org.elasticsearch.indices.IndicesService;
 import org.elasticsearch.indices.InvalidIndexNameException;
@@ -112,6 +115,7 @@ import static org.elasticsearch.cluster.routing.allocation.decider.MaxRetryAlloc
 import static org.elasticsearch.common.xcontent.XContentFactory.jsonBuilder;
 import static org.elasticsearch.index.IndexSettings.INDEX_REFRESH_INTERVAL_SETTING;
 import static org.elasticsearch.index.query.QueryBuilders.matchQuery;
+import static org.elasticsearch.index.shard.IndexShardTests.getEngineFromShard;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertAcked;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertAliasesExist;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertAliasesMissing;
@@ -3072,6 +3076,73 @@ public class SharedClusterSnapshotRestoreIT extends AbstractSnapshotIntegTestCas
         }
     }
 
+    public void testSnapshottingWithMissingSequenceNumbers() {
+        final String repositoryName = "test-repo";
+        final String snapshotName = "test-snap";
+        final String indexName = "test-idx";
+        final Client client = client();
+        final Path repo = randomRepoPath();
+
+        logger.info("-->  creating repository at {}", repo.toAbsolutePath());
+        assertAcked(client.admin().cluster().preparePutRepository(repositoryName)
+            .setType("fs").setSettings(Settings.builder()
+                .put("location", repo)
+                .put("compress", false)
+                .put("chunk_size", randomIntBetween(100, 1000), ByteSizeUnit.BYTES)));
+        logger.info("--> creating an index and indexing documents");
+        final String dataNode = internalCluster().getDataNodeInstance(ClusterService.class).localNode().getName();
+        final Settings settings =
+            Settings
+                .builder()
+                .put("index.number_of_shards", 1)
+                .put("index.number_of_replicas", 0)
+                .put("index.routing.allocation.include._name", dataNode)
+                .build();
+        createIndex(indexName, settings);
+        ensureGreen();
+        for (int i = 0; i < 5; i++) {
+            index(indexName, "_doc", Integer.toString(i), "foo", "bar" + i);
+        }
+
+        final Index index = resolveIndex(indexName);
+        final IndexShard primary = internalCluster().getInstance(IndicesService.class, dataNode).getShardOrNull(new ShardId(index, 0));
+        // create a gap in the sequence numbers
+        getEngineFromShard(primary).seqNoService().generateSeqNo();
+
+        for (int i = 5; i < 10; i++) {
+            index(indexName, "_doc", Integer.toString(i), "foo", "bar" + i);
+        }
+
+        refresh();
+
+        logger.info("--> snapshot");
+        CreateSnapshotResponse createSnapshotResponse = client.admin().cluster().prepareCreateSnapshot(repositoryName, snapshotName)
+            .setWaitForCompletion(true).setIndices(indexName).get();
+        assertThat(createSnapshotResponse.getSnapshotInfo().successfulShards(), greaterThan(0));
+        assertThat(createSnapshotResponse.getSnapshotInfo().successfulShards(),
+            equalTo(createSnapshotResponse.getSnapshotInfo().totalShards()));
+
+        logger.info("--> delete indices");
+        assertAcked(client.admin().indices().prepareDelete(indexName));
+
+        logger.info("--> restore all indices from the snapshot");
+        RestoreSnapshotResponse restoreSnapshotResponse = client.admin().cluster().prepareRestoreSnapshot("test-repo", "test-snap")
+            .setWaitForCompletion(true).execute().actionGet();
+        assertThat(restoreSnapshotResponse.getRestoreInfo().totalShards(), greaterThan(0));
+
+        logger.info("--> indexing some more");
+        for (int i = 10; i < 15; i++) {
+            index(indexName, "_doc", Integer.toString(i), "foo", "bar" + i);
+        }
+
+        IndicesStatsResponse stats = client().admin().indices().prepareStats(indexName).clear().get();
+        ShardStats shardStats = stats.getShards()[0];
+        assertTrue(shardStats.getShardRouting().primary());
+        assertThat(shardStats.getSeqNoStats().getLocalCheckpoint(), equalTo(15L)); // 15 indexed docs and one "missing" op.
+        assertThat(shardStats.getSeqNoStats().getGlobalCheckpoint(), equalTo(15L));
+        assertThat(shardStats.getSeqNoStats().getMaxSeqNo(), equalTo(15L));
+    }
+
     private void verifySnapshotInfo(final GetSnapshotsResponse response, final Map<String, List<String>> indicesPerSnapshot) {
         for (SnapshotInfo snapshotInfo : response.getSnapshots()) {
             final List<String> expected = snapshotInfo.indices();
diff --git a/test/framework/src/main/java/org/elasticsearch/test/ESIntegTestCase.java b/test/framework/src/main/java/org/elasticsearch/test/ESIntegTestCase.java
index be6a1b29681..e633f5adb70 100644
--- a/test/framework/src/main/java/org/elasticsearch/test/ESIntegTestCase.java
+++ b/test/framework/src/main/java/org/elasticsearch/test/ESIntegTestCase.java
@@ -738,6 +738,13 @@ public abstract class ESIntegTestCase extends ESTestCase {
         }
     }
 
+    /**
+     * creates an index with the given setting
+     */
+    public final void createIndex(String name, Settings indexSettings) {
+        assertAcked(prepareCreate(name).setSettings(indexSettings));
+    }
+
     /**
      * Creates a new {@link CreateIndexRequestBuilder} with the settings obtained from {@link #indexSettings()}.
      */