diff --git a/cmd/dep/ensure.go b/cmd/dep/ensure.go
index ef2793f706..fef9623607 100644
--- a/cmd/dep/ensure.go
+++ b/cmd/dep/ensure.go
@@ -160,6 +160,10 @@ func (cmd *ensureCommand) Run(ctx *dep.Ctx, args []string) error {
 	sm.UseDefaultSignalHandling()
 	defer sm.Release()
 
+	if err := dep.ValidateProjectRoots(ctx, p.Manifest, sm); err != nil {
+		return err
+	}
+
 	params := p.MakeParams()
 	if ctx.Verbose {
 		params.TraceLogger = ctx.Err
diff --git a/cmd/dep/status.go b/cmd/dep/status.go
index 973033662a..a849b15cb3 100644
--- a/cmd/dep/status.go
+++ b/cmd/dep/status.go
@@ -190,6 +190,10 @@ func (cmd *statusCommand) Run(ctx *dep.Ctx, args []string) error {
 	sm.UseDefaultSignalHandling()
 	defer sm.Release()
 
+	if err := dep.ValidateProjectRoots(ctx, p.Manifest, sm); err != nil {
+		return err
+	}
+
 	var buf bytes.Buffer
 	var out outputter
 	switch {
diff --git a/manifest.go b/manifest.go
index 11472a64a5..74a64da273 100644
--- a/manifest.go
+++ b/manifest.go
@@ -156,6 +156,29 @@ func validateManifest(s string) ([]error, error) {
 	return warns, nil
 }
 
+// ValidateProjectRoots validates the project roots present in manifest.
+func ValidateProjectRoots(c *Ctx, m *Manifest, sm gps.SourceManager) error {
+	projectRoots := make([]gps.ProjectRoot, 0, len(m.Constraints)+len(m.Ovr))
+	for pr := range m.Constraints {
+		projectRoots = append(projectRoots, pr)
+	}
+	for pr := range m.Ovr {
+		projectRoots = append(projectRoots, pr)
+	}
+
+	for _, pr := range projectRoots {
+		origPR, err := sm.DeduceProjectRoot(string(pr))
+		if err != nil {
+			return errors.Wrapf(err, "could not deduce project root for %s", pr)
+		}
+		if origPR != pr {
+			c.Err.Printf("dep: WARNING: name %q in Gopkg.toml should be project root", pr)
+		}
+	}
+
+	return nil
+}
+
 // readManifest returns a Manifest read from r and a slice of validation warnings.
 func readManifest(r io.Reader) (*Manifest, []error, error) {
 	buf := &bytes.Buffer{}
diff --git a/manifest_test.go b/manifest_test.go
index c79f5e02b1..f206db8b82 100644
--- a/manifest_test.go
+++ b/manifest_test.go
@@ -5,7 +5,10 @@
 package dep
 
 import (
+	"bytes"
 	"errors"
+	"io/ioutil"
+	"log"
 	"reflect"
 	"strings"
 	"testing"
@@ -372,3 +375,110 @@ func TestValidateManifest(t *testing.T) {
 		}
 	}
 }
+
+func TestValidateProjectRoots(t *testing.T) {
+	cases := []struct {
+		name      string
+		manifest  Manifest
+		wantError bool
+		wantWarn  []string
+	}{
+		{
+			name:      "empty Manifest",
+			manifest:  Manifest{},
+			wantError: false,
+			wantWarn:  []string{},
+		},
+		{
+			name: "valid project root",
+			manifest: Manifest{
+				Constraints: map[gps.ProjectRoot]gps.ProjectProperties{
+					gps.ProjectRoot("github.com/goland/dep"): {
+						Constraint: gps.Any(),
+					},
+				},
+			},
+			wantError: false,
+			wantWarn:  []string{},
+		},
+		{
+			name: "invalid project roots in Constraints and Overrides",
+			manifest: Manifest{
+				Constraints: map[gps.ProjectRoot]gps.ProjectProperties{
+					gps.ProjectRoot("github.com/golang/dep/foo"): {
+						Constraint: gps.Any(),
+					},
+					gps.ProjectRoot("github.com/golang/go/xyz"): {
+						Constraint: gps.Any(),
+					},
+					gps.ProjectRoot("github.com/golang/fmt"): {
+						Constraint: gps.Any(),
+					},
+				},
+				Ovr: map[gps.ProjectRoot]gps.ProjectProperties{
+					gps.ProjectRoot("github.com/golang/mock/bar"): {
+						Constraint: gps.Any(),
+					},
+					gps.ProjectRoot("github.com/golang/mock"): {
+						Constraint: gps.Any(),
+					},
+				},
+			},
+			wantError: false,
+			wantWarn: []string{
+				"name \"github.com/golang/dep/foo\" in Gopkg.toml should be project root",
+				"name \"github.com/golang/mock/bar\" in Gopkg.toml should be project root",
+				"name \"github.com/golang/go/xyz\" in Gopkg.toml should be project root",
+			},
+		},
+		{
+			name: "invalid source path",
+			manifest: Manifest{
+				Constraints: map[gps.ProjectRoot]gps.ProjectProperties{
+					gps.ProjectRoot("github.com/golang"): {
+						Constraint: gps.Any(),
+					},
+				},
+			},
+			wantError: true,
+			wantWarn:  []string{},
+		},
+	}
+
+	h := test.NewHelper(t)
+	defer h.Cleanup()
+
+	h.TempDir("src")
+	pwd := h.Path(".")
+
+	// Capture the stderr to verify the warnings
+	stderrOutput := &bytes.Buffer{}
+	errLogger := log.New(stderrOutput, "", 0)
+	ctx := &Ctx{
+		GOPATH: pwd,
+		Out:    log.New(ioutil.Discard, "", 0),
+		Err:    errLogger,
+	}
+
+	sm, err := ctx.SourceManager()
+	h.Must(err)
+	defer sm.Release()
+
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			// Empty the buffer for every case
+			stderrOutput.Reset()
+			err := ValidateProjectRoots(ctx, &c.manifest, sm)
+			if err != nil && !c.wantError {
+				t.Fatalf("Unexpected error while validating project roots: %q", err)
+			}
+
+			warnings := stderrOutput.String()
+			for _, warn := range c.wantWarn {
+				if !strings.Contains(warnings, warn) {
+					t.Fatalf("Expected ValidateProjectRoot warnings to contain: %q", warn)
+				}
+			}
+		})
+	}
+}