diff --git a/pkg/app/application_test.go b/pkg/app/application_test.go
index 555f38111..077ccf185 100644
--- a/pkg/app/application_test.go
+++ b/pkg/app/application_test.go
@@ -19,6 +19,7 @@ package app
 import (
 	"encoding/base64"
 	"reflect"
+	"strings"
 	"testing"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
@@ -197,6 +198,27 @@ func TestResources1(t *testing.T) {
 	}
 }
 
+func TestResourceNotFound(t *testing.T) {
+	l := loadertest.NewFakeLoader("/testpath")
+	err := l.AddFile("/testpath/"+constants.KustomizationFileName, []byte(kustomizationContent1))
+	if err != nil {
+		t.Fatalf("Failed to setup fake ldr.")
+	}
+	fakeFs := fs.MakeFakeFS()
+	fakeFs.Mkdir("/")
+	app, err := NewApplication(l, fakeFs)
+	if err != nil {
+		t.Fatalf("Unexpected construction error %v", err)
+	}
+	_, err = app.MakeCustomizedResMap()
+	if err == nil {
+		t.Fatalf("Didn't get the expected error for an unknown resource")
+	}
+	if !strings.Contains(err.Error(), `cannot read file "/testpath/deployment.yaml"`) {
+		t.Fatalf("Unpexpected error message %q", err)
+	}
+}
+
 func TestRawResources1(t *testing.T) {
 	expected := resmap.ResMap{
 		resource.NewResId(deploy, "dply1"): resource.NewResourceFromMap(
diff --git a/pkg/resmap/resmap.go b/pkg/resmap/resmap.go
index cb09a6d37..995c81e27 100644
--- a/pkg/resmap/resmap.go
+++ b/pkg/resmap/resmap.go
@@ -211,10 +211,14 @@ func newResourceSliceFromBytes(in []byte) ([]*resource.Resource, error) {
 	return result, nil
 }
 
-// MergeWithoutOverride combines multiple ResMap instances, failing on key collision.
+// MergeWithoutOverride combines multiple ResMap instances, failing on key collision
+// and skipping nil maps. In case if all of the maps are nil, an empty ResMap is returned.
 func MergeWithoutOverride(maps ...ResMap) (ResMap, error) {
 	result := ResMap{}
 	for _, m := range maps {
+		if m == nil {
+			continue
+		}
 		for id, res := range m {
 			if _, found := result[id]; found {
 				return nil, fmt.Errorf("id '%q' already used", id)
@@ -226,14 +230,21 @@ func MergeWithoutOverride(maps ...ResMap) (ResMap, error) {
 }
 
 // MergeWithOverride combines multiple ResMap instances, allowing and sometimes
-// demanding certain collisions.
+// demanding certain collisions and skipping nil maps.
+// In case if all of the maps are nil, an empty ResMap is returned.
 // When looping over the instances to combine them, if a resource id for resource X
 // is found to be already in the combined map, then the behavior field for X
 // must be BehaviorMerge or BehaviorReplace.  If X is not in the map, then it's
 // behavior cannot be merge or replace.
 func MergeWithOverride(maps ...ResMap) (ResMap, error) {
 	result := maps[0]
+	if result == nil {
+		result = ResMap{}
+	}
 	for _, m := range maps[1:] {
+		if m == nil {
+			continue
+		}
 		for id, r := range m {
 			matchedId := result.FindByGVKN(id)
 			if len(matchedId) == 1 {
diff --git a/pkg/resmap/resmap_test.go b/pkg/resmap/resmap_test.go
index 774a32198..bba8c8c93 100644
--- a/pkg/resmap/resmap_test.go
+++ b/pkg/resmap/resmap_test.go
@@ -202,6 +202,22 @@ func TestMergeWithoutOverride(t *testing.T) {
 	if !reflect.DeepEqual(merged, expected) {
 		t.Fatalf("%#v doesn't equal expected %#v", merged, expected)
 	}
+	input3 := []ResMap{merged, nil}
+	merged1, err := MergeWithoutOverride(input3...)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if !reflect.DeepEqual(merged1, expected) {
+		t.Fatalf("%#v doesn't equal expected %#v", merged1, expected)
+	}
+	input4 := []ResMap{nil, merged}
+	merged2, err := MergeWithoutOverride(input4...)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if !reflect.DeepEqual(merged2, expected) {
+		t.Fatalf("%#v doesn't equal expected %#v", merged2, expected)
+	}
 }
 
 func TestMergeWithOverride(t *testing.T) {
@@ -262,4 +278,20 @@ func TestMergeWithOverride(t *testing.T) {
 	if !reflect.DeepEqual(merged, expected) {
 		t.Fatalf("%#v doesn't equal expected %#v", merged, expected)
 	}
+	input3 := []ResMap{merged, nil}
+	merged1, err := MergeWithOverride(input3...)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if !reflect.DeepEqual(merged1, expected) {
+		t.Fatalf("%#v doesn't equal expected %#v", merged1, expected)
+	}
+	input4 := []ResMap{nil, merged}
+	merged2, err := MergeWithOverride(input4...)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if !reflect.DeepEqual(merged2, expected) {
+		t.Fatalf("%#v doesn't equal expected %#v", merged2, expected)
+	}
 }