Abstract:The utility of inter-simple sequence repeat(ISSR) DNA polymorphism to distinguish 6 taxa (Sonneratia caseolaris, S. paracaseolaris, S.alba, S.hainanensis, S.ovata, S.apetala) in the genus Sonneratia was investigated. The ISSR standardized procedure and the fingerprints database of Sonneratia species were established. 11 ISSR primers used produced 71 species-specific markers for the six Sonneratia species, including 23 specific to S.apetala, 16 specific to S.hainanensis, 15 specific to S.caseolaris, 6 specific to S. alba, 6 specific to S.paracaseolaris and 5 specific to S.ovata. According to these special markers, the six Sonneratia species could be identified quickly and accurately. It was shown that the ISSR technique is a reliable and effective tool to differentiate the Sonneratia species.