diff --git a/pkg/resmap/resmap.go b/pkg/resmap/resmap.go
index d0a2586fd..60ec6f131 100644
--- a/pkg/resmap/resmap.go
+++ b/pkg/resmap/resmap.go
@@ -140,6 +140,18 @@ func (m ResMap) insert(newName string, obj *unstructured.Unstructured) error {
 	return nil
 }
 
+// FilterBy returns a ResMap containing ResIds with the same namespace and nameprefix
+// with the inputId
+func (m ResMap) FilterBy(inputId resource.ResId) ResMap {
+	result := ResMap{}
+	for id, res := range m {
+		if id.Namespace() == inputId.Namespace() && id.HasSamePrefix(inputId) {
+			result[id] = res
+		}
+	}
+	return result
+}
+
 // NewResourceSliceFromPatches returns a slice of resources given a patch path slice from a kustomization file.
 func NewResourceSliceFromPatches(
 	loader loader.Loader, paths []patch.PatchStrategicMerge) ([]*resource.Resource, error) {
diff --git a/pkg/resource/resid.go b/pkg/resource/resid.go
index 5104a81cd..563e8701e 100644
--- a/pkg/resource/resid.go
+++ b/pkg/resource/resid.go
@@ -97,10 +97,35 @@ func (n ResId) Namespace() string {
 
 // CopyWithNewPrefix make a new copy from current ResId and append a new prefix
 func (n ResId) CopyWithNewPrefix(p string) ResId {
-	return ResId{gvk: n.gvk, name: n.name, prefix: p + n.prefix, namespace: n.namespace}
+	return ResId{gvk: n.gvk, name: n.name, prefix: n.concatePrefix(p), namespace: n.namespace}
 }
 
 // CopyWithNewNamespace make a new copy from current ResId and set a new namespace
 func (n ResId) CopyWithNewNamespace(ns string) ResId {
 	return ResId{gvk: n.gvk, name: n.name, prefix: n.prefix, namespace: ns}
 }
+
+// HasSamePrefix check if two ResIds have the same leading prefix
+func (n ResId) HasSamePrefix(id ResId) bool {
+	prefixes1 := n.prefixList()
+	prefixes2 := id.prefixList()
+	return len(prefixes1) == 0 || len(prefixes2) == 0 || prefixes1[0] == prefixes2[0]
+}
+
+func (n ResId) concatePrefix(p string) string {
+	if p == "" {
+		return n.prefix
+	}
+	if n.prefix == "" {
+		return p
+	}
+	return p + ":" + n.prefix
+}
+
+func (n ResId) prefixList() []string {
+	var plist []string
+	if n.prefix == "" {
+		return plist
+	}
+	return strings.Split(n.prefix, ":")
+}
diff --git a/pkg/transformers/namereference.go b/pkg/transformers/namereference.go
index 008f76fc4..89e887b01 100644
--- a/pkg/transformers/namereference.go
+++ b/pkg/transformers/namereference.go
@@ -21,6 +21,7 @@ import (
 	"fmt"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/resmap"
+	"github.com/kubernetes-sigs/kustomize/pkg/resource"
 	"k8s.io/apimachinery/pkg/runtime/schema"
 )
 
@@ -58,7 +59,7 @@ func (o *nameReferenceTransformer) Transform(m resmap.ResMap) error {
 					continue
 				}
 				err := mutateField(objMap, path.Path, path.CreateIfNotPresent,
-					o.updateNameReference(referencePathConfig.referencedGVK, m))
+					o.updateNameReference(referencePathConfig.referencedGVK, m.FilterBy(id)))
 				if err != nil {
 					return err
 				}
@@ -81,9 +82,21 @@ func (o *nameReferenceTransformer) updateNameReference(
 				continue
 			}
 			if id.Name() == s {
+				err := o.detectConflict(id, m, s)
+				if err != nil {
+					return nil, err
+				}
 				return res.GetName(), nil
 			}
 		}
 		return in, nil
 	}
 }
+
+func (o *nameReferenceTransformer) detectConflict(id resource.ResId, m resmap.ResMap, name string) error {
+	matchedIds := m.FindByGVKN(id)
+	if len(matchedIds) > 1 {
+		return fmt.Errorf("detected conflicts when resolving name references %s:\n%v", name, matchedIds)
+	}
+	return nil
+}