Abstract: Pengze crucian carp (Carassius auratus of pengze), a popular cultural fish in China, is an endemic bisexual populationwith natural gynogenetic reproduction mode.Interestingly, natural populations of this fish consist of a minor portion (no morethan 20%)of males.It was reported that Pengze crucian carp had a high genetic kinship to the clone A in the silver cruciancarp, and belonged to one of clones of the silver crucian carp.However, the previous investigations on the morphology and cyto-genetics indicated that therewere two distinguishable gynogenetic clones of pengze crucian carp, named cloneH and clone L, re-spectively.It is necessary for using direct molecular evidence to prove if the population of Pengze crucian carp includes somegynogenetic clones.In this study, the two clones(H and L)of gynogenetic pengze crucian carp were analyzed by the random am-plified polymorphic DNA(RAPD) technique, using 30 10-nucleotide-long random primers, and twenty-eight primers producedwell-amplified DNA fragments.Similar banding patterns were observed among individualswithin each gynogenetic clone, whereasobvious differences were detected between the two gynogenetic clones.Using these informative band patterns produced by the 28primers, all individual, a total of 2,154 distinguishable DNA fragments(215 per individual), including universal and specific,with data coded as a vector of 1 or 0, representing band presence or absence, respectively.Genetic distance matrices amongthese individuals of two clones were estimated based on the method of Lynch.The results indicated that the genetic distances ofclone H are 0.013761 -0.044084, clone L are 0.014085 -0.046948, and between clone H and clone L are 0.333333 -0.368910.The average genetic distances within clone H and Lwere 0.018070?.015489 and 0.017827?.015203, respec-tively, and which was 0.352511?.009692 between the two clones.Average genetic distances within and between the twoclones clearly indicated their intraclonal homogeneity and interclonal heterogeneity.A total of 91 polymorphic fragments werescored from28 primers after excluding bands that were monomorphic for the two clones.These polymorphic fragments showed thegenetic diversity of the population of Pengze crucian carp.Some primers, for example Opj15, Opp8, Opq11, Opq14 and so on,produced abundant and reproducible banding patterns that could be efficiently used to discriminate between the two gynogeneticclones.At the same time, according to the genetic distance among these individuals of two clones, a phylogenetic tree was con-structed using Neighbor-Joining program in MEGA3.1.The dendrogram of 10 individuals in the two clones showed their originand relationship.All individuals in the cloneHwere clustered into onegroup, and all individuals from the clone Lwere clusteredinto anothergroup.The difference based on detection of RAPD molecularmarkers provided more evidence for the genetic diversi-ty of Pengze crucian carp, and identified two gynogenetic cloneswere obviously existent in the population of Pengze crucian carp.This study results further indicate that it is a general phenomena with natural gynogenetic fishes including a lot of gynogeneticclones.As the silver crucian carp, the genetic diversity of the gynogenetic Pengze crucian carp will likely benefit evolutionary ge-netics studies of unisexual vertebrates and selective breeding of Pengze crucian carp.