diff --git a/api/builtins/PatchTransformer.go b/api/builtins/PatchTransformer.go
index cb7a83c01..67e49fb05 100644
--- a/api/builtins/PatchTransformer.go
+++ b/api/builtins/PatchTransformer.go
@@ -8,6 +8,7 @@ import (
 	"strings"
 
 	jsonpatch "github.com/evanphx/json-patch"
+	"github.com/pkg/errors"
 	"sigs.k8s.io/kustomize/api/filters/patchjson6902"
 	"sigs.k8s.io/kustomize/api/filters/patchstrategicmerge"
 	"sigs.k8s.io/kustomize/api/resmap"
@@ -101,7 +102,31 @@ func (p *PatchTransformerPlugin) transformStrategicMerge(m resmap.ResMap, patch
 		patchCopy.SetGvk(res.GetGvk())
 		err := p.applySMPatch(res, patchCopy)
 		if err != nil {
-			return err
+			// Check for an error string from UnmarshalJSON that's indicative
+			// of an object that's missing basic KRM fields, and thus may have been
+			// entirely deleted (an acceptable outcome).  This error handling should
+			// be deleted along with use of ResMap and apimachinery functions like
+			// UnmarshalJSON.
+			if !strings.Contains(err.Error(), "Object 'Kind' is missing") {
+				// Some unknown error, let it through.
+				return err
+			}
+			if len(res.Map()) != 0 {
+				return errors.Wrapf(
+					err, "with unexpectedly non-empty object map of size %d",
+					len(res.Map()))
+			}
+			// Fall through to handle deleted object.
+		}
+		if len(res.Map()) == 0 {
+			// This means all fields have been removed from the object.
+			// This can happen if a patch required deletion of the
+			// entire resource (not just a part of it).  This means
+			// the overall resmap must shrink by one.
+			err = m.Remove(res.CurId())
+			if err != nil {
+				return err
+			}
 		}
 	}
 	return nil
diff --git a/plugin/builtin/patchtransformer/PatchTransformer.go b/plugin/builtin/patchtransformer/PatchTransformer.go
index c2e917492..bde29cf61 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer.go
@@ -9,6 +9,7 @@ import (
 	"strings"
 
 	jsonpatch "github.com/evanphx/json-patch"
+	"github.com/pkg/errors"
 	"sigs.k8s.io/kustomize/api/filters/patchjson6902"
 	"sigs.k8s.io/kustomize/api/filters/patchstrategicmerge"
 	"sigs.k8s.io/kustomize/api/resmap"
@@ -105,7 +106,31 @@ func (p *plugin) transformStrategicMerge(m resmap.ResMap, patch *resource.Resour
 		patchCopy.SetGvk(res.GetGvk())
 		err := p.applySMPatch(res, patchCopy)
 		if err != nil {
-			return err
+			// Check for an error string from UnmarshalJSON that's indicative
+			// of an object that's missing basic KRM fields, and thus may have been
+			// entirely deleted (an acceptable outcome).  This error handling should
+			// be deleted along with use of ResMap and apimachinery functions like
+			// UnmarshalJSON.
+			if !strings.Contains(err.Error(), "Object 'Kind' is missing") {
+				// Some unknown error, let it through.
+				return err
+			}
+			if len(res.Map()) != 0 {
+				return errors.Wrapf(
+					err, "with unexpectedly non-empty object map of size %d",
+					len(res.Map()))
+			}
+			// Fall through to handle deleted object.
+		}
+		if len(res.Map()) == 0 {
+			// This means all fields have been removed from the object.
+			// This can happen if a patch required deletion of the
+			// entire resource (not just a part of it).  This means
+			// the overall resmap must shrink by one.
+			err = m.Remove(res.CurId())
+			if err != nil {
+				return err
+			}
 		}
 	}
 	return nil
diff --git a/plugin/builtin/patchtransformer/PatchTransformer_test.go b/plugin/builtin/patchtransformer/PatchTransformer_test.go
index ac1bbb750..84dcf85f3 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer_test.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer_test.go
@@ -508,6 +508,61 @@ spec:
 `)
 }
 
+func TestPatchTransformerWithPatchDelete(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("PatchTransformer")
+	defer th.Reset()
+
+	th.RunTransformerAndCheckResult(`
+apiVersion: builtin
+kind: PatchTransformer
+metadata:
+  name: notImportantHere
+target:
+  name: myDeploy
+  kind: Deployment
+patch: |-
+  apiVersion: apps/v1
+  metadata:
+    name: myDeploy
+  kind: Deployment
+  $patch: delete
+`, someDeploymentResources, `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  labels:
+    new-label: new-value
+  name: yourDeploy
+spec:
+  replica: 1
+  template:
+    metadata:
+      labels:
+        new-label: new-value
+    spec:
+      containers:
+      - image: nginx:1.7.9
+        name: nginx
+---
+apiVersion: apps/v1
+kind: MyKind
+metadata:
+  label:
+    old-label: old-value
+  name: myDeploy
+spec:
+  template:
+    metadata:
+      labels:
+        old-label: old-value
+    spec:
+      containers:
+      - image: nginx
+        name: nginx
+`)
+}
+
 const anIngressResource = `apiVersion: networking.k8s.io/v1beta1
 kind: Ingress
 metadata:
diff --git a/plugin/builtin/patchtransformer/go.mod b/plugin/builtin/patchtransformer/go.mod
index 9715015dc..3ed291da5 100644
--- a/plugin/builtin/patchtransformer/go.mod
+++ b/plugin/builtin/patchtransformer/go.mod
@@ -6,6 +6,7 @@ require (
 	github.com/evanphx/json-patch v4.5.0+incompatible
 	sigs.k8s.io/kustomize/api v0.6.2
 	sigs.k8s.io/kustomize/kyaml v0.8.1
+	github.com/pkg/errors v0.8.1
 	sigs.k8s.io/yaml v1.2.0
 )