Genetic diversity, reproductive mode diversity and their relationships were studied by molecular marker techniques in natural gynogenetic silver crucian carp (Carassius auratus gibelio Bloch) based on understanding the research advances about sex evolution and evolutionary genetics of unisexual animals. The studies were mainly focused on two phenomena that there exist various gynogenetic clones and male individuals in the natural populations. Three major achievements were obtained in this dissertation. First, genetic heterogeneity and their relationships among five gynogenetic clones of silver crucian carp were analyzed by RAPD and microsatellite techniques. A total of 88 RAPD markers and 23 microsatellite markers were scored from 24 RAPD primers and 5 pairs of microsatellite primers. The amplified patterns and the constructed dendrograms clearly indicated their intraclonal homogeneity, interclonal heterogeneity, and their phylogenetic relationships. Five typical RAPD markers were selected for molecular cloning and sequencing. According to the nucleotide sequences, five pairs of SCAR primers were designed and synthesized to identify the specific fragments in these gynogenetic clones. Five gynogenetic clones could be easily discriminated by the 5 SCAR markers. Second, a lot of artificial propagation experiments were performed between different gynogenetic clones to analyze whether or not genetic recombination occurs by utilizing the identified RAPD and SCAR markers. Direct molecular genetic evidence for gonochoristic reproduction was revealed in the gynogenetic silver crucian carp, and a previous hypothesis that the silver crucian carp might reproduce both gynogenetically and gonochoristically was conformed. The responding mechanism of two different reproductive development modes might be the first discovery in vertebrates so far. On the other hand, gonochoristic reproduction produces abundant genetic variation, and creates genetic diversity. Based on the discovery, a preliminary model of reproductive modes was proposed, which can direct the breeding and propagation of silver crucian carp. Third, growth differences between females and males were analyzed, and sex-specific DNA fragments were attempted to screen by 120 RAPD primer amplification in the gonochoristic offspring. A 0.9 kb DNA fragment specific for females was screened in the RAPD pattern amplified by primer Oph-8, and was confirmed by Southern blot. The female-specific fragment was composed of 898 bp. According to the nucleotide sequences, one pair of PCR primers were designed and synthesized to detect the female-specific fragment in gonochoristic offspring. Additionally, the primers can be used to discriminate between the normal and the sex-revised males, because the revised males contain the female-specific fragment.