diff --git a/cmd/notation/cert/delete_test.go b/cmd/notation/cert/delete_test.go
index 310d1ddaf..3f2c72909 100644
--- a/cmd/notation/cert/delete_test.go
+++ b/cmd/notation/cert/delete_test.go
@@ -14,8 +14,12 @@
 package cert
 
 import (
+	"os"
+	"path/filepath"
 	"reflect"
 	"testing"
+
+	"github.com/notaryproject/notation-go/dir"
 )
 
 func TestCertDeleteCommand(t *testing.T) {
@@ -51,3 +55,46 @@ func TestCertDeleteCommand_MissingArgs(t *testing.T) {
 		t.Fatal("Parse Args expected error, but ok")
 	}
 }
+
+// A named store of "." or ".." must not resolve to the store type directory
+// or to the parent of it, which would delete other trust stores.
+func TestCertDelete_DotNamedStoresDoNotTouchOtherStores(t *testing.T) {
+	for _, namedStore := range []string{".", ".."} {
+		t.Run(namedStore, func(t *testing.T) {
+			oldConfigDir := dir.UserConfigDir
+			t.Cleanup(func() { dir.UserConfigDir = oldConfigDir })
+			dir.UserConfigDir = t.TempDir()
+
+			certFiles := make([]string, 0, 2)
+			for _, store := range [][2]string{{"ca", "store1"}, {"tsa", "store2"}} {
+				storeDir, err := dir.ConfigFS().SysPath(dir.TrustStoreDir, "x509", store[0], store[1])
+				if err != nil {
+					t.Fatal(err)
+				}
+				if err := os.MkdirAll(storeDir, 0o700); err != nil {
+					t.Fatal(err)
+				}
+				certFile := filepath.Join(storeDir, "cert.pem")
+				if err := os.WriteFile(certFile, []byte("cert"), 0o600); err != nil {
+					t.Fatal(err)
+				}
+				certFiles = append(certFiles, certFile)
+			}
+
+			err := deleteCerts(&certDeleteOpts{
+				storeType:  "ca",
+				namedStore: namedStore,
+				all:        true,
+				confirmed:  true,
+			})
+			if err == nil {
+				t.Fatalf("deleteCerts() with the named store %q expected an error, but got nil", namedStore)
+			}
+			for _, certFile := range certFiles {
+				if _, statErr := os.Stat(certFile); statErr != nil {
+					t.Errorf("%s was removed: %v", certFile, statErr)
+				}
+			}
+		})
+	}
+}
diff --git a/cmd/notation/internal/truststore/truststore.go b/cmd/notation/internal/truststore/truststore.go
index 881a312a2..c7ff90291 100644
--- a/cmd/notation/internal/truststore/truststore.go
+++ b/cmd/notation/internal/truststore/truststore.go
@@ -226,7 +226,11 @@ func IsValidStoreType(storeType string) bool {
 	return false
 }
 
-// IsValidFileName checks if a file name is cross-platform compatible
+var validFileName = regexp.MustCompile(`^[a-zA-Z0-9_.-]+$`)
+
+// IsValidFileName checks if a file name is cross-platform compatible.
+// "." and ".." are rejected, because they refer to a directory and not to a
+// file name inside of one.
 func IsValidFileName(fileName string) bool {
-	return regexp.MustCompile(`^[a-zA-Z0-9_.-]+$`).MatchString(fileName)
+	return fileName != "." && fileName != ".." && validFileName.MatchString(fileName)
 }
diff --git a/cmd/notation/internal/truststore/truststore_test.go b/cmd/notation/internal/truststore/truststore_test.go
index b8aab3635..01cea0fba 100644
--- a/cmd/notation/internal/truststore/truststore_test.go
+++ b/cmd/notation/internal/truststore/truststore_test.go
@@ -119,3 +119,28 @@ func TestDeleteAllCerts(t *testing.T) {
 		}
 	})
 }
+
+func TestIsValidFileName(t *testing.T) {
+	tests := []struct {
+		name     string
+		fileName string
+		want     bool
+	}{
+		{"letters, digits and separators", "ok-1_.x", true},
+		{"hidden style name", ".hidden", true},
+		{"two dots inside a name", "a..b", true},
+		{"empty", "", false},
+		{"current directory", ".", false},
+		{"parent directory", "..", false},
+		{"slash", "a/b", false},
+		{"backslash", `a\b`, false},
+		{"space", "a b", false},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := IsValidFileName(tt.fileName); got != tt.want {
+				t.Fatalf("IsValidFileName(%q) = %v, want %v", tt.fileName, got, tt.want)
+			}
+		})
+	}
+}