Abstract: The genetic diversity and genetic structure of Wenzhou buffaloes distributed in Pingyang， Ruian， Yongjia， Yueqing and Wenzhou in Zhejiang province were analyzed by ISSR-PCR. A total of 154 polymorphic loci of 186 were amplified using 9 primers selected from 22 primers. Percentage of polymorphism loci （PPL） was 82.80％， observed number of alleles was 1.8420， effective number of alleles was 1.5702， Neis gene diversity was 0.3108， Shannons information index was 0.4687， all of the genetic parameters in population level were higher than individual level. Genetic differentiation level （Gst） calculated according to Neis gene diversity was 0.1840， which suggested that 18.40% genetic variation was present in populations. UPMGA cluster analysis in the strains of Wenzhou buffaloes also demonstrated that Wenzhou buffaloes has lower genetic diversity among the populations and the genetic variation mainly exists in the individual ones.

Key words: Wenzhou buffaloes, ISSR marker, genetic structure, genetic differentiation, genetic diversity