Background <p>The Sichuan taimen (<i>Hucho bleekeri</i> Kimura) is a critically endangered fish species that has attracted significant attention and is classified as a national first-level protected species in China. Despite its ecological importance, genomic resources for the Sichuan taimen and its closely related species are limited, which hampers effective conservation efforts. A comprehensive understanding of the genomic characteristics of this species, particularly those related to its evolutionary adaptations and population dynamics, is essential for improving conservation strategies.</p> Results <p>We present the first chromosome-level genome of the Sichuan taimen, with a final genome size of approximately 3.45 Gb. Notably, tandem repetitive sequences constitute 44.47% of the genome and significantly influence its genomic architecture and functional organization. Among these, VNTRs account for the majority of the tandem repeats, which Likely contributes to the relatively large genome size. Positive selection analysis revealed genes associated with immune responses and neurobiological functions, potentially facilitating adaptation to the unique environmental conditions of mountain stream habitats. Additionally, the divergence time between the Siberian taimen and the Sichuan taimen was estimated to be approximately 2.34 Mya, with a notable decline in their effective population size occurring around 1 Mya.</p> Conclusions <p>The genome assembly of the Sichuan taimen provides insights into its evolutionary adaptations, highlighting the functional significance of tandem repeats and positively selected genes. These findings establish a genomic foundation for elucidating its survival mechanisms in a unique habitat, and emphasize the critical role of integrating genomic data into conservation strategies to enhance the management of Sichuan taimen populations and contribute to the conservation of other endangered salmonid species.</p>