Genetic structure of an endangered endemic fish (Gobiocypris rarus) in the upper Yangtze River

► We examined the population genetic structure of rare minnow in the upper Yangtze. ► Low to moderate levels of genetic differentiation and an IBD pattern were revealed. ► Two genetic clusters may be highly correlated with the evolution of water systems. ► Five populations of Gobiocypris rarus are suggested to be protected in prior.