The Qinghai–Tibet Plateau and surrounding montane valleys comprise one of the world’s most pronounced freshwater environmental gradients, where cold, intense UV radiation, variable dissolved oxygen, and heterogeneous hydrodynamics interact with drainage reorganization and connectivity constraints. Schizothoracinae are among the most representative endemic lineages in these systems, combining exceptional lineage diversity with pervasive polyploid genomic backgrounds. Here we synthesize schizothoracine research through an “environment–evolution–conservation” framework, linking (i) taxonomic and phylogenetic foundations under pervasive convergence, cryptic diversity, and hybridization; (ii) geologic history and drainage evolution as drivers of radiation and gene exchange; (iii) polyploidy, post-WGD structural remodeling, and early rediploidization as a testable process rather than a static ploidy fact; and (iv) omics resources and analytical pipelines that enable verifiable evidence chains across comparative genomics, population genomics, and tissue-level stress responses. Across major stressors, recurrent molecular themes emerge for cold-associated metabolic remodeling and UV-associated DNA repair and genome maintenance, whereas hypoxia-related signals are often inconsistent, plausibly reflecting strong spatiotemporal heterogeneity and multi-route physiological accommodation. We further connect molecular candidates to functional outcomes using reusable phenotypic evidence streams, including geometric morphometrics, high-throughput phenotyping, otolith microchemistry, and age–growth life-history syndromes of slow growth and longevity. Finally, we translate population structure into operational MU/ESU delineation and propose an auditable, iterative management checklist centered on MU-aligned stocking, connectivity performance metrics during critical seasonal windows, and quantified habitat restoration targets. We conclude by outlining priorities to raise evidentiary strength across basins: chromosome-level genomes across lineages, systematic SV/TE comparisons, standardized stressor–phenotype–transcriptome designs, and intensified sampling in geomorphic transition zones and putative hybrid regions to enable cumulative, decision-ready synthesis.

The Qinghai–Tibet Plateau and surrounding mountain regions form one of the world’s most distinctive freshwater environmental gradients. Schizothoracinae are among the most representative endemic fish lineages in these systems and provide a useful model for studying how drainage history, genome evolution, adaptation, and conservation interact. In this review, we synthesize schizothoracine research within an environment–evolution–conservation framework. We examine how drainage history and connectivity shape divergence and gene exchange, how polyploidy and genome remodeling provide the genomic background for adaptive inference, and how phenotypic and population-genomic evidence can be translated into conservation units and management priorities. Across current studies, cold-associated metabolic remodeling and UV-related DNA damage response and repair emerge as the most recurrent molecular themes, whereas hypoxia-related signals are more context-dependent. We further show that morphology, otolith chemistry, age–growth traits, and population structure can strengthen MU/ESU interpretation when integrated with genomic evidence. Future progress will depend on broader chromosome-level genome coverage, more systematic comparison of structural genomic variation, standardized stressor-linked designs, and denser sampling in geomorphic transition zones and putative hybrid regions.