Abstract:A total of 95 rice varieties were collected including four compatibility groups of indica compatible varieties （ICV）, japonica compatible varieties （JCV）, wide compatible varieties （WCV） and incompatible varieties （NCV）. Genetic variation and genetic structure among the four groups were evaluated by using isozyme markers. Ten isozymes gave rise to 55 alleles in 34 loci of which 15 （P = 44.12%） were polymorphic. The average expected heterozygosity ranged from 0.354 to 0.456 at the group level, and 0.454 at the species level. AMOVA analysis showed that 80.21% of genetic variance distributed within groups, and only 19.79% among groups. The variation of genetic distance between groups ranged from 0.1129 to 0.3673, and the gene flow ranged from 1.0242 to 2.5451. UPGMA cluster analysis based on Nei＇s genetic distance could divide the four groups into two clusters:( Ⅰ ) wcv and JCV, ( Ⅱ ) ICV and NCV.