Megalobrama, a genus of cyprinid fish, is an important freshwater economic fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni and M. pellegrini. The results indicated that different geographical Megalobrama populations were separated into six subgroups and M. skolkovii was more closely related to M. pellegrini than other species. Megalobrama was originally distributed in the Pearl River, some spread to Hainan Island due to sea-level fall during the glacial period and others spread to northern China. The introgression provided an important genetic variation source of M. skolkovii populations. M. amblycephala enhanced energy metabolism mainly through fatty acid degradation pathways, while M. skolkovii used cholesterol metabolism pathway to regulate lipid absorption. Taken together, our results provide a valuable genomic resource for future genetic studies to improve genome-assisted breeding of Megalobrama species.