diff --git a/models/action.go b/models/action.go
index 318a5f6ad4..ed90ad900e 100644
--- a/models/action.go
+++ b/models/action.go
@@ -41,14 +41,14 @@ var (
 
 var (
 	// Same as Github. See https://help.github.com/articles/closing-issues-via-commit-messages
-	IssueCloseKeywords    = []string{"close", "closes", "closed", "fix", "fixes", "fixed", "resolve", "resolves", "resolved"}
-	IssueCloseKeywordsPat *regexp.Regexp
+	IssueCloseKeywords        = []string{"close", "closes", "closed", "fix", "fixes", "fixed", "resolve", "resolves", "resolved"}
+	IssueCloseKeywordsPat     *regexp.Regexp
 	IssueReferenceKeywordsPat *regexp.Regexp
 )
 
 func init() {
 	IssueCloseKeywordsPat = regexp.MustCompile(fmt.Sprintf(`(?i)(?:%s) \S+`, strings.Join(IssueCloseKeywords, "|")))
-	IssueReferenceKeywordsPat = regexp.MustCompile(fmt.Sprintf(`(?i)(?:) \S+`))
+	IssueReferenceKeywordsPat = regexp.MustCompile(`(?i)(?:)(^| )\S+`)
 }
 
 // Action represents user operation type and other information to repository.,
@@ -113,12 +113,14 @@ func (a Action) GetIssueInfos() []string {
 func updateIssuesCommit(userId, repoId int64, repoUserName, repoName string, commits []*base.PushCommit) error {
 	for _, c := range commits {
 		references := IssueReferenceKeywordsPat.FindAllString(c.Message, -1)
-		
+
+		// FIXME: should not be a reference when it comes with action.
+		// e.g. fixes #1 will not have duplicated reference message.
 		for _, ref := range references {
 			ref := ref[strings.IndexByte(ref, byte(' '))+1:]
 			ref = strings.TrimRightFunc(ref, func(c rune) bool {
-					return !unicode.IsDigit(c)
-				})
+				return !unicode.IsDigit(c)
+			})
 
 			if len(ref) == 0 {
 				continue
@@ -128,7 +130,7 @@ func updateIssuesCommit(userId, repoId int64, repoUserName, repoName string, com
 			if ref[0] == '#' {
 				ref = fmt.Sprintf("%s/%s%s", repoUserName, repoName, ref)
 			} else if strings.Contains(ref, "/") == false {
-				// We don't support User#ID syntax yet
+				// FIXME: We don't support User#ID syntax yet
 				// return ErrNotImplemented
 
 				continue
@@ -153,8 +155,8 @@ func updateIssuesCommit(userId, repoId int64, repoUserName, repoName string, com
 		for _, ref := range closes {
 			ref := ref[strings.IndexByte(ref, byte(' '))+1:]
 			ref = strings.TrimRightFunc(ref, func(c rune) bool {
-					return !unicode.IsDigit(c)
-				})
+				return !unicode.IsDigit(c)
+			})
 
 			if len(ref) == 0 {
 				continue
@@ -199,7 +201,7 @@ func updateIssuesCommit(userId, repoId int64, repoUserName, repoName string, com
 				}
 			}
 		}
-		
+
 	}
 
 	return nil
diff --git a/modules/base/markdown.go b/modules/base/markdown.go
index 4122098618..b5f397dce0 100644
--- a/modules/base/markdown.go
+++ b/modules/base/markdown.go
@@ -177,8 +177,8 @@ func RenderSha1CurrentPattern(rawBytes []byte, urlPrefix string) []byte {
 func RenderIssueIndexPattern(rawBytes []byte, urlPrefix string) []byte {
 	ms := issueIndexPattern.FindAll(rawBytes, -1)
 	for _, m := range ms {
-		rawBytes = bytes.Replace(rawBytes, m, []byte(fmt.Sprintf(
-			`<a href="%s/issues/%s">%s</a>`, urlPrefix, m[1:], m)), -1)
+		rawBytes = bytes.Replace(rawBytes, m, []byte(fmt.Sprintf(`<a href="%s/issues/%s">%s</a>`,
+			urlPrefix, strings.TrimPrefix(string(m[1:]), "#"), m)), -1)
 	}
 	return rawBytes
 }
diff --git a/routers/repo/view.go b/routers/repo/view.go
index cb689df6a0..cfe0fa010c 100644
--- a/routers/repo/view.go
+++ b/routers/repo/view.go
@@ -127,7 +127,6 @@ func Home(ctx *middleware.Context) {
 		entries.Sort()
 
 		files := make([][]interface{}, 0, len(entries))
-
 		for _, te := range entries {
 			if te.Type != git.COMMIT {
 				c, err := ctx.Repo.Commit.GetCommitOfRelPath(filepath.Join(treePath, te.Name()))
@@ -151,16 +150,6 @@ func Home(ctx *middleware.Context) {
 				files = append(files, []interface{}{te, git.NewSubModuleFile(c, sm.Url, te.Id.String())})
 			}
 		}
-
-		// Render issue index links.
-		for _, f := range files {
-			switch c := f[1].(type) {
-			case *git.Commit:
-				c.CommitMessage = c.CommitMessage
-			case *git.SubModuleFile:
-				c.CommitMessage = c.CommitMessage
-			}
-		}
 		ctx.Data["Files"] = files
 
 		var readmeFile *git.Blob
@@ -208,7 +197,6 @@ func Home(ctx *middleware.Context) {
 		}
 
 		lastCommit := ctx.Repo.Commit
-		lastCommit.CommitMessage = string(base.RenderIssueIndexPattern([]byte(lastCommit.CommitMessage), ctx.Repo.RepoLink))
 		if len(treePath) > 0 {
 			c, err := ctx.Repo.Commit.GetCommitOfRelPath(treePath)
 			if err != nil {