AbstractLeuciscus waleckiiis widely distributed in Northeast Asia and has high economic value. The population in Lake Dali Nur can adapt to extremely alkaline–saline water with bicarbonate over 50 mmol/L (pH 9.6), thus providing an exceptional model for exploring the mechanisms of adaptive evolution under extreme alkaline environments. Here, we assembled a high-quality chromosome-level reference genome forL. waleckiifrom Lake Dali Nur. Based on the resequencing of 85 individuals from divergent populations, the historical population size ofL. waleckiiin Lake Dali Nur dramatically expanded in a thousand years approximately 13,000 years ago and experienced a cliff recession in the process of adapting to the alkaline environment of Lake Dali Nur approximately 6,000 years ago. Genome scans between freshwater and alkaline populations further revealed the significant selective sweep regions from Lake Dali Nur, which harbor a set of candidate genes involved in hypoxia tolerance, ion transport, acid–base regulation, and nitrogen metabolism. 5 alkali population–specific nonsynonymous mutations were identified in CA15 gene copies. In addition, two sites with convergent amino acid mutation were detected in the RHCG-a gene among several alkali environment–adapted Cypriniformes fish. Our findings provide comprehensive insight into the genomic mechanisms ofL. waleckiiand reveal their adaptative evolution under extreme alkaline environments.