Abstract: Swamp eel (Monopterus albus) is an important freshwater culture fish in China and has the characteristic of hermaphroditism and natural sexual reversal. Currently, there is a lack of artificial varieties within swamp eel cultivation, and the fry of mainly rely on the wild catching. Gynogenesis, a method for rapidly obtaining fish population with stable heredity and excellent character, was explored in this study. Meiogynogenesis induction was established in swamp eel, resulting in the creation of three gynogenic populations characterized by deep-yellow coloration. Flow cytometry analysis showed that the cellular DNA contents of gynogenic eels were consistent with those of wild type fish, and chromosome counting confirmed the diploid nature with 48 chromosomes. Histological analysis demonstrated the development of ovaries in the gonads of gynogenic eels, indicating normal diploid functionality. Microsatellite diversity analysis showed that the effective number of alleles (N_e), Shannon’s information index (I), polymorphism information content (PIC), observed heterozygosity (H_o) and expected heterozygosity (H_e) in gynogenic eels were significantly lower than those in the wild population. The genetic homozygosity in gynogenetic eels exhibited a significant improvement. The genetic distance increased and the genetic similarity decreased between gynogenetic groups. In summary, the gynogenetic population of the deep-yellow swamp eels provides new materials for breeding excellent varieties.