An　auto　focusing　method　based　on　auto　focusing　window　selection　was　presented　according　to　the　imaging　principle　and　characteristics　of　fundus　images.　The　preliminary　focusing　window　is　extracted　through　the　focusing　window　selection　algorithm　based　on　local　entropy　with　improved　threshold.　The　final　window　is　located　through　multi-directional　stepping　algorithm.　The　image　sharpness　evaluation　function　combined　with　the　characteristics　of　local　contrast　sharpness　evaluation　function　and　gradient　vector　square　function　was　presented　according　to　low　contrast　fundus　images.　Experimental　results　show　that　the　presented　auto　focusing　window　selection　algorithm　ensure　the　stability　and　accuracy　for　the　focusing　window,　and　the　image　sharpness　evaluation　function　has　better　sensitiveness　for　low　contrast　fundus　images.　©,　2014,　Chinese　Optical　Society.　All　right　reserved.