diff --git a/commands.go b/commands.go
index bd10a33..5f1b473 100644
--- a/commands.go
+++ b/commands.go
@@ -918,12 +918,16 @@ func Update(ctx context.Context) ([]UpdateCheck, error) {
 			continue
 		}
 
-		ref := u.Entry.Source.Ref
-		if ref == "" {
-			ref = "main"
+		ref, err := resolveCloneRef(ctx, "https://github.com/"+owner+"/"+repo+".git", u.Entry.Source.Ref)
+		if err != nil {
+			continue
 		}
 
-		srcURL := "https://github.com/" + owner + "/" + repo + "/tree/" + ref + "/" + strings.TrimPrefix(u.Entry.SkillPath, "/")
+		srcURL := "https://github.com/" + owner + "/" + repo
+		if ref != "" {
+			srcURL += "/tree/" + ref
+		}
+		srcURL += "/" + strings.TrimPrefix(u.Entry.SkillPath, "/")
 		_, _ = Add(ctx, AddOptions{
 			Source:               srcURL,
 			Global:               true,
diff --git a/git.go b/git.go
index d0785d7..bc6e6b9 100644
--- a/git.go
+++ b/git.go
@@ -9,6 +9,8 @@ import (
 	"strings"
 )
 
+var ErrDefaultBranchNotFound = errors.New("default branch not found")
+
 type clonedRepo struct {
 	Dir string
 }
@@ -23,6 +25,26 @@ func cloneRepo(ctx context.Context, src SkillSource) (*clonedRepo, error) {
 		_ = os.RemoveAll(tmp)
 	}
 
+	repoURL := normalizeRepoURL(src)
+
+	args := []string{"clone", "--depth", "1"}
+	if src.Ref != "" {
+		args = append(args, "--branch", src.Ref)
+	}
+	args = append(args, repoURL, tmp)
+
+	cmd := exec.CommandContext(ctx, "git", args...)
+
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		cleanup()
+		return nil, errors.New("git clone failed: " + strings.TrimSpace(string(out)))
+	}
+
+	return &clonedRepo{Dir: tmp}, nil
+}
+
+func normalizeRepoURL(src SkillSource) string {
 	repoURL := src.SourceURL
 	if src.Type == SkillSourceTypeGitHub && src.Owner != "" && src.Repo != "" && !strings.HasPrefix(repoURL, "http") {
 		repoURL = "https://github.com/" + src.Owner + "/" + src.Repo + ".git"
@@ -36,21 +58,46 @@ func cloneRepo(ctx context.Context, src SkillSource) (*clonedRepo, error) {
 		repoURL = repoURL + ".git"
 	}
 
-	ref := src.Ref
-	if ref == "" {
-		ref = "main"
+	return repoURL
+}
+
+func resolveCloneRef(ctx context.Context, repoURL string, requestedRef string) (string, error) {
+	if requestedRef != "" {
+		return requestedRef, nil
 	}
 
-	args := []string{"clone", "--depth", "1", "--branch", ref, repoURL, tmp}
-	cmd := exec.CommandContext(ctx, "git", args...)
+	ref, err := detectDefaultBranch(ctx, repoURL)
+	if err != nil {
+		if errors.Is(err, ErrDefaultBranchNotFound) {
+			return "", nil
+		}
+		return "", err
+	}
+
+	return ref, nil
+}
 
+func detectDefaultBranch(ctx context.Context, repoURL string) (string, error) {
+	cmd := exec.CommandContext(ctx, "git", "ls-remote", "--symref", repoURL, "HEAD")
 	out, err := cmd.CombinedOutput()
 	if err != nil {
-		cleanup()
-		return nil, errors.New("git clone failed: " + strings.TrimSpace(string(out)))
+		return "", errors.New("git ls-remote failed: " + strings.TrimSpace(string(out)))
 	}
 
-	return &clonedRepo{Dir: tmp}, nil
+	for _, line := range strings.Split(string(out), "\n") {
+		if !strings.HasPrefix(line, "ref:") || !strings.Contains(line, "\tHEAD") {
+			continue
+		}
+
+		fields := strings.Fields(line)
+		if len(fields) < 2 {
+			continue
+		}
+
+		return strings.TrimPrefix(fields[1], "refs/heads/"), nil
+	}
+
+	return "", ErrDefaultBranchNotFound
 }
 
 func (r *clonedRepo) ResolveSubdir(subpath string) (string, error) {
diff --git a/git_test.go b/git_test.go
new file mode 100644
index 0000000..e9416e4
--- /dev/null
+++ b/git_test.go
@@ -0,0 +1,43 @@
+package skills
+
+import (
+	"context"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestDetectDefaultBranch(t *testing.T) {
+	tmp := t.TempDir()
+	remote := filepath.Join(tmp, "remote.git")
+	work := filepath.Join(tmp, "work")
+
+	runCmd(t, tmp, "git", "init", "--bare", remote)
+	runCmd(t, tmp, "git", "clone", remote, work)
+	runCmd(t, work, "git", "checkout", "-b", "master")
+	runCmd(t, work, "git", "config", "user.name", "tester")
+	runCmd(t, work, "git", "config", "user.email", "tester@example.com")
+	runCmd(t, work, "git", "commit", "--allow-empty", "-m", "init")
+	runCmd(t, work, "git", "push", "-u", "origin", "master")
+
+	branch, err := detectDefaultBranch(context.Background(), remote)
+	if err != nil {
+		t.Fatalf("detectDefaultBranch returned error: %v", err)
+	}
+
+	if branch != "master" {
+		t.Fatalf("expected master, got %q", branch)
+	}
+}
+
+func runCmd(t *testing.T, dir string, name string, args ...string) {
+	t.Helper()
+
+	cmd := exec.Command(name, args...)
+	cmd.Dir = dir
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("%s %s failed: %v\n%s", name, strings.Join(args, " "), err, out)
+	}
+}
diff --git a/source.go b/source.go
index 42eef91..70d09de 100644
--- a/source.go
+++ b/source.go
@@ -58,7 +58,6 @@ func ParseSource(input string) (SkillSource, error) {
 					SourceURL: in,
 					Owner:     parts[0],
 					Repo:      strings.TrimSuffix(parts[1], ".git"),
-					Ref:       "main",
 				}, nil
 			}
 		}
@@ -111,7 +110,6 @@ func ParseSource(input string) (SkillSource, error) {
 			SourceURL:   "https://github.com/" + repoPart,
 			Owner:       owner,
 			Repo:        repo,
-			Ref:         "main",
 			SkillFilter: skillFilter,
 		}, nil
 	}
diff --git a/source_test.go b/source_test.go
index 350557e..192cb79 100644
--- a/source_test.go
+++ b/source_test.go
@@ -32,6 +32,21 @@ func TestParseSource_GitHubShorthand(t *testing.T) {
 	if src.Owner != "vercel-labs" || src.Repo != "agent-skills" {
 		t.Fatalf("owner/repo mismatch: %s/%s", src.Owner, src.Repo)
 	}
+
+	if src.Ref != "" {
+		t.Fatalf("expected empty ref for default branch discovery, got %q", src.Ref)
+	}
+}
+
+func TestParseSource_GitHubRepoURL(t *testing.T) {
+	src, err := ParseSource("https://github.com/a/b")
+	if err != nil {
+		t.Fatalf("expected nil err, got %v", err)
+	}
+
+	if src.Type != SkillSourceTypeGitHub || src.Ref != "" {
+		t.Fatalf("expected github source with empty ref, got %#v", src)
+	}
 }
 
 func TestParseSource_GitHubTreeURL(t *testing.T) {