The blunt snout bream, Megalobrama amblycephala, is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. The whole genome sequecing of Megalobrama amblycephala provide novel functional insights into the evolution of cyprinids. Importantly, the M. amblycephala genome data come up with novel insights shedding light on the adaptation to herbivorous nutrition and evolution and formation of iintermuscular bones.