Northern pike (Esox lucius) is widely distributed in the high latitudes of the northern hemisphere. In Xinjiang of China, the original record only distributed the Irtysh River, which has now spread to the main water bodies in northern Xinjiang and Bosten Lake in Southern Xinjiang. The number, extent and source of introductions of pike into Xinjiang waterways besides Irtysh River remain currently unknown. Understanding the genetic diversity, population structure and connectivity of the various populations could help us better trace the spread pattern of northern pike in Xinjiang, China. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD) and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population.