diff --git a/kyaml/kio/byteio_reader.go b/kyaml/kio/byteio_reader.go
index 9036b1739cf..7cc96ba6cca 100644
--- a/kyaml/kio/byteio_reader.go
+++ b/kyaml/kio/byteio_reader.go
@@ -316,8 +316,14 @@ func (r *ByteReader) decode(originalYAML string, index int, decoder *yaml.Decode
 		r.SetAnnotations = map[string]string{}
 	}
 	if !r.OmitReaderAnnotations {
-		r.SetAnnotations[kioutil.IndexAnnotation] = fmt.Sprintf("%d", index)
-		r.SetAnnotations[kioutil.LegacyIndexAnnotation] = fmt.Sprintf("%d", index)
+		err := kioutil.CopyLegacyAnnotations(n)
+		if err != nil {
+			return nil, err
+		}
+		if val, ok := n.GetAnnotations()[kioutil.IndexAnnotation]; !ok || val == "" {
+			r.SetAnnotations[kioutil.IndexAnnotation] = fmt.Sprintf("%d", index)
+			r.SetAnnotations[kioutil.LegacyIndexAnnotation] = fmt.Sprintf("%d", index)
+		}
 
 		if r.PreserveSeqIndent {
 			// derive and add the seqindent annotation
diff --git a/kyaml/kio/kioutil/kioutil.go b/kyaml/kio/kioutil/kioutil.go
index bcd97303007..542e28f1373 100644
--- a/kyaml/kio/kioutil/kioutil.go
+++ b/kyaml/kio/kioutil/kioutil.go
@@ -55,6 +55,9 @@ func GetFileAnnotations(rn *yaml.RNode) (string, string, error) {
 func CopyLegacyAnnotations(rn *yaml.RNode) error {
 	meta, err := rn.GetMeta()
 	if err != nil {
+		if err != yaml.ErrMissingMetadata {
+			return nil
+		}
 		return err
 	}
 	if err := copyAnnotations(meta, rn, LegacyPathAnnotation, PathAnnotation); err != nil {