In the present study, two groups with different genetic backgrounds were obtained by intergeneric crossing Megalobrama amblycephala (♀)×Erythroculter ilishaeformis (♂). Our results show that fertilization rate (90.0%) and hatching rate (80.6%) in the intergeneric cross group were high. Hybrid A (96.2%) and hybrid B (3.8%) were obtained. The morphological characters of hybrid A were intermediate between those of the parents, and hybrid B had the same morphological characters as the M. amblycephala female parent. Relative DNA content of the hybrids was examined by flow cytometry. The results show that hybrids A and B were diploid and had the same DNA content as their parents. Two pairs of specific loci (TTF6 and TTF10) were screened by simple sequence repeat analysis. The results indicate that hybrid A inherited genetic material from both parents, whereas hybrid B only inherited maternal genetic material, indicating gynogenetic progeny. Hybrid A grew faster than either M. amblycephala or E. ilishaeformis, suggesting a clear growth advantage in earthen ponds. Our results provide basic data on a novel hybrid strain between Parabramis pekinensis and Erythroculter ilishaeformis. In addition, production of gynogenetic progeny can be applied to establish a pure line of M. amblycephala.