Abstract: Phenotypic differences of fin isozymes (EST,LDH,SOD,IDHP,MDH) and fin proteins in four different gynogenetic clones of silver crucian carp,red common carp and multiple tetraploid allogynogenetic crucian carp were comparatively analysed through polyacrylamide gradient gel electrophoresis.The results suggested that major part of phenotypic differences among the individuals of multiple tetraploid allogynogenetic crucian carp came from intraspecific genetic differences of silver crucian carp (different gynogenetic clones).The multiple tetraploid allogynogenetic crucian carp whose female parents were clone D silver crucian carp showed individual differences in EST isozymes,and these differences were related to the polymorphism of EST isozymes in red common carp.Therefore,these heterogeneity among the individuals that included genetic effect come from male parents.Moreover,it was found that the fin proteins and fin EST isozymes manifested obvious individual differences,which could be used as genetic marker to distinguish different multiple tetraploid allogynogenetic crucian carp.