Abstract: Allogynogenetic gibel carp (Carassius gibelio) is an important freshwater aquaculture fish in China. In order to clarify its current status of its germplasm resources in breeding population from Hubei Province, we collected six allogynogenetic gibel carp breeding populations to compare their biological characteristics and quality traits. We also investigated genetic diversity and identified varieties and clones by genome re-sequencing. The results indicated that a total of 10 clones were identified based on the SNPs from genome re-sequencing of 180 allogynogenetic gibel carps, including two allogynogenetic gibel carp “CASⅢ” subclones, five allogynogenetic gibel carp “CASⅤ” subclones, and three other clones. Genetic diversity analysis showed that single nucleotide density (SNP/Kb), single nucleotide polymorphism (p), polymorphism information content (PIC), and observed heterozygosity (H_o) were 11.17, 0.0050, 0.4332, and 0.5612, respectively. Phylogenetic tree and principal component analysis revealed moderate to significant genetic differentiation and a significant cross clustering phenomenon. Combined with distribution of allogynogenetic gibel carp clones, we indicated that there was a certain genetic mixing phenomenon in the breeding parents of allogynogenetic gibel carp except for LZH and ZD populations. The apparent morphology differences existed among the different populations, with body height/length and head length/body length can be used as reference indicators for morphology judgment of allogynogenetic gibel carp. The crude fat content in muscle nutrients varied significantly between “CASⅢ” and “CASⅤ”, but there was no significant difference in crude protein content. Additionally, the content of 17 fatty acids in muscle showed a significant difference among different clones, as well as the total amount of EPA and DHA, varied among different populations. This study not only benefits the rational development and protection of germplasm resources, but also contributes to the new varieties breeding and the sustainable development of allogynogenetic gibel carp aquaculture.