Studying Xanthomonas strains of 4 species and 29 pathovars by isoelectric focusing, it was shown that the protein patterns were very different among the species and pathovars. Through cluster analysis of IEF date, it was found that the protein pattern differences among certain pathovars were no fewer than that among the species. It revealed that some pathovars could become to be species. There were few differences of 6 protein bands among X. campestris pv. cerealis, X. campestris pv. undulosa and X. campestris pv. hordei which cause bacterial black cheff, so the classification of the three pathovars need to be re-considered. It also showed that isoelectric focusing could be used to classify Xanthomonas below species.