diff --git a/meta/data.go b/meta/data.go
index d7ef4b0947..8c05964a76 100644
--- a/meta/data.go
+++ b/meta/data.go
@@ -240,7 +240,14 @@ func (data *Data) ShardGroups(database, policy string) ([]ShardGroupInfo, error)
 	} else if rpi == nil {
 		return nil, ErrRetentionPolicyNotFound
 	}
-	return rpi.ShardGroups, nil
+	groups := make([]ShardGroupInfo, 0, len(rpi.ShardGroups))
+	for _, g := range rpi.ShardGroups {
+		if g.Deleted() {
+			continue
+		}
+		groups = append(groups, g)
+	}
+	return groups, nil
 }
 
 // ShardGroupByTimestamp returns the shard group on a database and policy for a given timestamp.
@@ -331,10 +338,10 @@ func (data *Data) DeleteShardGroup(database, policy string, id uint64) error {
 		return ErrRetentionPolicyNotFound
 	}
 
-	// Find shard group by ID and remove it.
+	// Find shard group by ID and set its deletion timestamp.
 	for i := range rpi.ShardGroups {
 		if rpi.ShardGroups[i].ID == id {
-			rpi.ShardGroups = append(rpi.ShardGroups[:i], rpi.ShardGroups[i+1:]...)
+			rpi.ShardGroups[i].DeletedAt = time.Now().UTC()
 			return nil
 		}
 	}
@@ -568,7 +575,7 @@ func NewRetentionPolicyInfo(name string) *RetentionPolicyInfo {
 // ShardGroupByTimestamp returns the shard group in the policy that contains the timestamp.
 func (rpi *RetentionPolicyInfo) ShardGroupByTimestamp(timestamp time.Time) *ShardGroupInfo {
 	for i := range rpi.ShardGroups {
-		if rpi.ShardGroups[i].Contains(timestamp) {
+		if rpi.ShardGroups[i].Contains(timestamp) && !rpi.ShardGroups[i].Deleted() {
 			return &rpi.ShardGroups[i]
 		}
 	}
@@ -609,12 +616,16 @@ func shardGroupDuration(d time.Duration) time.Duration {
 	return 1 * time.Hour
 }
 
-// ShardGroupInfo represents metadata about a shard group.
+// ShardGroupInfo represents metadata about a shard group. The DeletedAt field is important
+// because it makes it clear that a ShardGroup has been marked as deleted, and allow the system
+// to be sure that a ShardGroup is not simply missing. If the DeletedAt is set, the system can
+// safely delete any associated shards.
 type ShardGroupInfo struct {
 	ID        uint64
 	StartTime time.Time
 	EndTime   time.Time
 	Shards    []ShardInfo
+	DeletedAt time.Time
 }
 
 // Contains return true if the shard group contains data for the timestamp.
@@ -627,6 +638,11 @@ func (sgi *ShardGroupInfo) Overlaps(min, max time.Time) bool {
 	return !sgi.StartTime.After(max) && sgi.EndTime.After(min)
 }
 
+// Deleted returns whether this ShardGroup has been deleted.
+func (sgi *ShardGroupInfo) Deleted() bool {
+	return !sgi.DeletedAt.IsZero()
+}
+
 // clone returns a deep copy of sgi.
 func (sgi ShardGroupInfo) clone() ShardGroupInfo {
 	other := sgi
diff --git a/meta/data_test.go b/meta/data_test.go
index a15cdd5d0d..4998b0a32c 100644
--- a/meta/data_test.go
+++ b/meta/data_test.go
@@ -365,8 +365,9 @@ func TestData_DeleteShardGroup(t *testing.T) {
 
 	if err := data.DeleteShardGroup("db0", "rp0", 1); err != nil {
 		t.Fatal(err)
-	} else if len(data.Databases[0].RetentionPolicies[0].ShardGroups) != 0 {
-		t.Fatalf("unexpected shard groups: %#v", data.Databases[0].RetentionPolicies[0].ShardGroups)
+	}
+	if sg := data.Databases[0].RetentionPolicies[0].ShardGroups[0]; !sg.Deleted() {
+		t.Fatalf("shard group not correctly flagged as deleted")
 	}
 }
 
diff --git a/meta/store.go b/meta/store.go
index d67d2148cf..ff9ce5fa08 100644
--- a/meta/store.go
+++ b/meta/store.go
@@ -525,7 +525,7 @@ func (s *Store) CreateShardGroupIfNotExists(database, policy string, timestamp t
 	// Try to find shard group locally first.
 	if sgi, err := s.ShardGroupByTimestamp(database, policy, timestamp); err != nil {
 		return nil, err
-	} else if sgi != nil {
+	} else if sgi != nil && !sgi.Deleted() {
 		return sgi, nil
 	}
 
diff --git a/services/retention/service.go b/services/retention/service.go
index 56777d09a9..883c606980 100644
--- a/services/retention/service.go
+++ b/services/retention/service.go
@@ -107,16 +107,17 @@ func (s *Service) deleteShards() {
 		case <-ticker.C:
 			s.logger.Println("retention policy shard deletion commencing")
 
-			// Build a list of all shard IDs that exist.
-			shardIDs := make(map[uint64]struct{}, 0)
+			deletedShardIDs := make(map[uint64]struct{}, 0)
 			s.MetaStore.VisitShardGroups(func(d meta.DatabaseInfo, r meta.RetentionPolicyInfo, g meta.ShardGroupInfo) {
-				for _, sh := range g.Shards {
-					shardIDs[sh.ID] = struct{}{}
+				if g.Deleted() {
+					for _, sh := range g.Shards {
+						deletedShardIDs[sh.ID] = struct{}{}
+					}
 				}
 			})
 
 			for _, id := range s.TSDBStore.ShardIDs() {
-				if _, ok := shardIDs[id]; !ok {
+				if _, ok := deletedShardIDs[id]; ok {
 					if err := s.TSDBStore.DeleteShard(id); err != nil {
 						s.logger.Printf("failed to delete shard ID %d: %s", id, err.Error())
 						continue