diff --git a/examples/flappy/crt.go b/examples/flappy/crt.go
index ff38b3c49..5f2d8d831 100644
--- a/examples/flappy/crt.go
+++ b/examples/flappy/crt.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 // Reference: a public domain CRT effect
diff --git a/examples/flappy/main.go b/examples/flappy/main.go
index 7ca80406a..6b8ab9436 100644
--- a/examples/flappy/main.go
+++ b/examples/flappy/main.go
@@ -43,6 +43,8 @@ var flagCRT = flag.Bool("crt", false, "enable the CRT effect")
 //go:embed crt.go
 var crtGo []byte
 
+//ebitengine:shaderfile crt.go
+
 func floorDiv(x, y int) int {
 	d := x / y
 	if d*y == x || x >= 0 {
diff --git a/examples/shader/chromaticaberration.go b/examples/shader/chromaticaberration.go
index abbf49ced..f5689a99a 100644
--- a/examples/shader/chromaticaberration.go
+++ b/examples/shader/chromaticaberration.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/examples/shader/default.go b/examples/shader/default.go
index 4d5387a59..1c7f70197 100644
--- a/examples/shader/default.go
+++ b/examples/shader/default.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/examples/shader/dissolve.go b/examples/shader/dissolve.go
index 6388d0d19..006061a26 100644
--- a/examples/shader/dissolve.go
+++ b/examples/shader/dissolve.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/examples/shader/lighting.go b/examples/shader/lighting.go
index 9d6761cd0..32e905957 100644
--- a/examples/shader/lighting.go
+++ b/examples/shader/lighting.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/examples/shader/main.go b/examples/shader/main.go
index d8a75d98c..7aae6fe53 100644
--- a/examples/shader/main.go
+++ b/examples/shader/main.go
@@ -50,6 +50,17 @@ var (
 	water_go []byte
 )
 
+// These directives are used for an shader analyzer in the future.
+// See also #3157.
+
+//ebitengine:shaderfile default.go
+//ebitengine:shaderfile texel.go
+//ebitengine:shaderfile lighting.go
+//ebitengine:shaderfile radialblur.go
+//ebitengine:shaderfile chromaticaberration.go
+//ebitengine:shaderfile dissolve.go
+//ebitengine:shaderfile water.go
+
 const (
 	screenWidth  = 640
 	screenHeight = 480
diff --git a/examples/shader/radialblur.go b/examples/shader/radialblur.go
index 89f82cc72..f6e648e31 100644
--- a/examples/shader/radialblur.go
+++ b/examples/shader/radialblur.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/examples/shader/texel.go b/examples/shader/texel.go
index eaca326e5..7e06e0488 100644
--- a/examples/shader/texel.go
+++ b/examples/shader/texel.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/examples/shader/water.go b/examples/shader/water.go
index 564ad43b9..59685bdd7 100644
--- a/examples/shader/water.go
+++ b/examples/shader/water.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 //kage:unit pixels
 
 package main
diff --git a/internal/shaderlister/main.go b/internal/shaderlister/main.go
index 9799ccc4c..f744e9ec5 100644
--- a/internal/shaderlister/main.go
+++ b/internal/shaderlister/main.go
@@ -17,6 +17,7 @@ package main
 import (
 	"bufio"
 	"encoding/json"
+	"errors"
 	"flag"
 	"fmt"
 	"go/ast"
@@ -25,6 +26,7 @@ import (
 	"go/types"
 	"log/slog"
 	"os"
+	"path/filepath"
 	"regexp"
 	"strings"
 
@@ -94,7 +96,7 @@ func xmain() error {
 	}
 
 	pkgs, err := packages.Load(&packages.Config{
-		Mode: packages.NeedName | packages.NeedImports | packages.NeedDeps | packages.NeedTypes | packages.NeedSyntax | packages.NeedTypesInfo | packages.NeedEmbedFiles,
+		Mode: packages.NeedName | packages.NeedImports | packages.NeedDeps | packages.NeedTypes | packages.NeedSyntax | packages.NeedTypesInfo,
 	}, flag.Args()...)
 	if err != nil {
 		return err
@@ -180,16 +182,16 @@ func isStandardImportPath(path string) bool {
 }
 
 const (
-	shaderSourceDirective   = "ebitengine:shadersource"
-	embeddedShaderDirective = "ebitengine:embeddedshader"
+	shaderSourceDirective = "ebitengine:shadersource"
+	shaderFileDirective   = "ebitengine:shaderfile"
 )
 
 var (
-	reShaderSourceDirective   = regexp.MustCompile(`(?m)^\s*//` + regexp.QuoteMeta(shaderSourceDirective))
-	reEmbeddedShaderDirective = regexp.MustCompile(`(?m)^\s*//` + regexp.QuoteMeta(embeddedShaderDirective))
+	reShaderSourceDirective = regexp.MustCompile(`(?m)^\s*//` + regexp.QuoteMeta(shaderSourceDirective) + `$`)
+	reShaderFileDirective   = regexp.MustCompile(`(?m)^\s*//` + regexp.QuoteMeta(shaderFileDirective) + ` (.+)$`)
 )
 
-func hasShaderDirectiveInComment(commentGroup *ast.CommentGroup) bool {
+func hasShaderSourceDirectiveInComment(commentGroup *ast.CommentGroup) bool {
 	for _, line := range commentGroup.List {
 		if reShaderSourceDirective.MatchString(line.Text) {
 			return true
@@ -210,8 +212,54 @@ func appendShaderSources(shaders []Shader, pkg *packages.Package) ([]Shader, err
 		return ok
 	}
 
-	var genDeclStack []*ast.GenDecl
+	// Resolve ebitengine:shaderfile directives.
+	for _, f := range pkg.Syntax {
+		for _, c := range f.Comments {
+			for _, l := range c.List {
+				m := reShaderFileDirective.FindStringSubmatch(l.Text)
+				if len(m) == 0 {
+					continue
+				}
+				pattern := filepath.Join(pkg.Dir, filepath.FromSlash(m[1]))
+				stat, err := os.Stat(pattern)
+				if err == nil && stat.IsDir() {
+					// If the pattern is a directory, read all files in the directory recursively.
+					if err := filepath.WalkDir(pattern, func(path string, d os.DirEntry, err error) error {
+						if err != nil {
+							return err
+						}
+						if d.IsDir() {
+							return nil
+						}
+						shaders, err = appendShaderFromFile(shaders, pkg.PkgPath, path)
+						if err != nil {
+							return err
+						}
+						return nil
+					}); err != nil {
+						return nil, err
+					}
+					continue
+				}
+				if err != nil && !errors.Is(err, os.ErrNotExist) {
+					return nil, err
+				}
+				paths, err := filepath.Glob(pattern)
+				if err != nil {
+					return nil, err
+				}
+				for _, path := range paths {
+					shaders, err = appendShaderFromFile(shaders, pkg.PkgPath, path)
+					if err != nil {
+						return nil, err
+					}
+				}
+			}
+		}
+	}
 
+	// Resolve ebitengine:shadersource directives.
+	var genDeclStack []*ast.GenDecl
 	in := inspector.New(pkg.Syntax)
 	in.Nodes([]ast.Node{
 		(*ast.GenDecl)(nil),
@@ -228,7 +276,7 @@ func appendShaderSources(shaders []Shader, pkg *packages.Package) ([]Shader, err
 				// If the GenDecl is with parentheses (e.g. `const ( ... )`), check the GenDecl's comment.
 				// The directive doesn't work, so if the directive is found, warn it.
 				if genDecl.Lparen != token.NoPos {
-					if genDecl.Doc != nil && hasShaderDirectiveInComment(genDecl.Doc) {
+					if genDecl.Doc != nil && hasShaderSourceDirectiveInComment(genDecl.Doc) {
 						pos := pkg.Fset.Position(genDecl.Doc.Pos())
 						slog.Warn(fmt.Sprintf("misplaced %s directive", shaderSourceDirective),
 							"package", pkg.PkgPath,
@@ -240,7 +288,7 @@ func appendShaderSources(shaders []Shader, pkg *packages.Package) ([]Shader, err
 					if genDecl.Doc == nil {
 						return false
 					}
-					if !hasShaderDirectiveInComment(genDecl.Doc) {
+					if !hasShaderSourceDirectiveInComment(genDecl.Doc) {
 						return false
 					}
 				}
@@ -264,7 +312,7 @@ func appendShaderSources(shaders []Shader, pkg *packages.Package) ([]Shader, err
 				if spec.Doc == nil {
 					return false
 				}
-				if !hasShaderDirectiveInComment(spec.Doc) {
+				if !hasShaderSourceDirectiveInComment(spec.Doc) {
 					return false
 				}
 			}
@@ -335,21 +383,19 @@ func appendShaderSources(shaders []Shader, pkg *packages.Package) ([]Shader, err
 		}
 	})
 
-	for _, file := range pkg.EmbedFiles {
-		content, err := os.ReadFile(file)
-		if err != nil {
-			return nil, err
-		}
-		if !reEmbeddedShaderDirective.Match(content) {
-			continue
-		}
-		shaders = append(shaders, Shader{
-			Package: pkg.PkgPath,
-			File:    file,
-			Source:  string(content),
-		})
-	}
+	return shaders, nil
+}
 
+func appendShaderFromFile(shaders []Shader, pkgPath string, filePath string) ([]Shader, error) {
+	content, err := os.ReadFile(filePath)
+	if err != nil {
+		return nil, err
+	}
+	shaders = append(shaders, Shader{
+		Package: pkgPath,
+		File:    filePath,
+		Source:  string(content),
+	})
 	return shaders, nil
 }
 
diff --git a/internal/shaderlister/shaderlister_test.go b/internal/shaderlister/shaderlister_test.go
index 6550ba24c..8bdbdf55d 100644
--- a/internal/shaderlister/shaderlister_test.go
+++ b/internal/shaderlister/shaderlister_test.go
@@ -82,7 +82,7 @@ func TestRun(t *testing.T) {
 	})
 
 	if got, want := len(filteredShaders), 9; got != want {
-		t.Fatalf("len(shaders): got: %d, want: %d", got, want)
+		t.Errorf("len(shaders): got: %d, want: %d", got, want)
 	}
 
 	for i, s := range filteredShaders {
diff --git a/internal/shaderlister/shaderlistertest/def.go b/internal/shaderlister/shaderlistertest/def.go
index 4054d4ae2..aac55ae88 100644
--- a/internal/shaderlister/shaderlistertest/def.go
+++ b/internal/shaderlister/shaderlistertest/def.go
@@ -15,8 +15,6 @@
 package shaderlistertest
 
 import (
-	"embed"
-
 	"github.com/hajimehoshi/ebiten/v2/internal/shaderlister/shaderlistertest2"
 )
 
@@ -71,8 +69,7 @@ const (
 	_, _ = "ignored", "ignored again" // multiple consts are ignored to avoid confusion.
 )
 
-//go:embed *kage.go
-var embed_go embed.FS
+//ebitengine:shaderfile *_kage.go
+//ebitengine:shaderfile resource
 
-//go:embed resource
-var embed2_go embed.FS
+//ebitengine:shaderfile nonexistent.go
diff --git a/internal/shaderlister/shaderlistertest/embed2_kage.go b/internal/shaderlister/shaderlistertest/dummy2_kage.go
similarity index 95%
rename from internal/shaderlister/shaderlistertest/embed2_kage.go
rename to internal/shaderlister/shaderlistertest/dummy2_kage.go
index 1bfd3ed9c..336ab1974 100644
--- a/internal/shaderlister/shaderlistertest/embed2_kage.go
+++ b/internal/shaderlister/shaderlistertest/dummy2_kage.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 package main
 
 // shader 8
diff --git a/internal/shaderlister/shaderlistertest/embed_kage.go b/internal/shaderlister/shaderlistertest/dummy_kage.go
similarity index 95%
rename from internal/shaderlister/shaderlistertest/embed_kage.go
rename to internal/shaderlister/shaderlistertest/dummy_kage.go
index 3a3a1b439..e309403d4 100644
--- a/internal/shaderlister/shaderlistertest/embed_kage.go
+++ b/internal/shaderlister/shaderlistertest/dummy_kage.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 package main
 
 // shader 7
diff --git a/internal/shaderlister/shaderlistertest/embed_notkage.go b/internal/shaderlister/shaderlistertest/dummy_notkage.go
similarity index 83%
rename from internal/shaderlister/shaderlistertest/embed_notkage.go
rename to internal/shaderlister/shaderlistertest/dummy_notkage.go
index 66bbc9971..99c4594de 100644
--- a/internal/shaderlister/shaderlistertest/embed_notkage.go
+++ b/internal/shaderlister/shaderlistertest/dummy_notkage.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-// This file lacks the directive `ebitengine:embeddedshader`, so this is not considered as a shader file by shaderlister.
-
 package main
 
 // shader 0
diff --git a/internal/shaderlister/shaderlistertest/resource/embed_kage.go b/internal/shaderlister/shaderlistertest/resource/dummy_kage.go
similarity index 95%
rename from internal/shaderlister/shaderlistertest/resource/embed_kage.go
rename to internal/shaderlister/shaderlistertest/resource/dummy_kage.go
index 46bc1d959..846090733 100644
--- a/internal/shaderlister/shaderlistertest/resource/embed_kage.go
+++ b/internal/shaderlister/shaderlistertest/resource/dummy_kage.go
@@ -14,8 +14,6 @@
 
 //go:build ignore
 
-//ebitengine:embeddedshader
-
 package main
 
 // shader 9
diff --git a/internal/shaderlister/shaderlistertest/resource/embed_notkage.go b/internal/shaderlister/shaderlistertest/resource/embed_notkage.go
deleted file mode 100644
index 66bbc9971..000000000
--- a/internal/shaderlister/shaderlistertest/resource/embed_notkage.go
+++ /dev/null
@@ -1,21 +0,0 @@
-// Copyright 2025 The Ebitengine Authors
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-//go:build ignore
-
-// This file lacks the directive `ebitengine:embeddedshader`, so this is not considered as a shader file by shaderlister.
-
-package main
-
-// shader 0