To provide more information on the molecular identification methods for the genus Alexanderium, some SSR were screened from ESTs database about Alexandrium tamarense by means of bioinformatics. The genetic diversity was analyzed among 4 strains of A. tamarense, 2 strains of A. affine and 1 strain of A. catenella by capillary electrophoresis. Totally 222 SSR were discovered, one SSR per 18.5 kb in average. The trinucleotide repeats accounting for 48.2%, were dominant among the repeat motifs, of which CTG/CAG was the most type. Twelve of primers were further screened for the analysis of genetic diversity. Low level of genetic diversity was observed in intraspecies of Alexandrium spp., with the ratio of polymorphic primers of 41.67% and Neis gene diversity of 0.2130 in average. In contrast, higher genetic diversity was observed in interspecies of Alexandrium spp. with ratio of polymorphic primers of 75% and Neis gene diversity of 0.4643. The interspecies genetic coefficient of differentiation was higher with the average level of 0.7051. According to the dendrogram of these seven strains, A. tamarense CCMP116 and A. affine CCMP112 greatly closed to each other. A. tamarense ATHK9301, CCMP1598 and ATDH01 clustered together. A. catenella ACDH01 and A. tamarense distributed in the two branches. These results suggested that the SSR marker was a potentially useful method in the study of within-species genetic variability of Alexanderium spp.