In this study, we present a de novo genome assembly of Gymnocypris przewalski using long‐read PacBio sequencing technology with Genome-wide high throughput chromosome conformation capture correction. The assembly resulted in a high sequence contiguity and accuracy with 23 chromosomes and a genome size of 945 Mb. This work is the first chromosome‐level genome study of Schizothoracine fishes from the Qinghai-tibet plateau (QTP). Phylogenetic analysis showed that the species differentiation events between G. przewalskii and Cyprinus carpio occurred at 24.06 Mya ago, which reveals geographic isolation of Schizothoracine fishes in QTP lift; the unique gene analysis found that most of these genes enriched in membrane transport and immune defensive pathways such as ABC transporters, bile secretion and cell adhesion molecules. Moreover, this genome resource is a key to understanding evolutionary adaptation to high altitudes, disentangling complex evolutionary histories, and will be useful for research on species diversity and resource conservation of Schizothoracine fishes on the QTP.