Background <p>Genetic data have long been applied in conservation and management for threatened and endangered species to track effects of inbreeding, hybridization, and population structure. However, when a reference genome is lacking, there is inadequate information to confidently predict extinction risk or potential for local adaptation to varying environmental factors. A reference genome provides information about the identity and function of key gene families that likely affect organismal performance in nature. A well-resolved genome is therefore vital to future conservation planning for protected species. Gila Trout have undergone severe genetic and demographic bottlenecks due to habitat fragmentation and climate-based drought and wildfires in the Gila national forest, NM. The species is currently managed under a recovery program that works to ensure the preservation of five genetically and morphologically distinct Gila Trout lineages.</p> Results <p>Here we present a chromosome-level assembly and annotation of the genome of Gila Trout <i>Oncorhynchus gilae</i>, a threatened trout species closely related to the Rainbow Trout. We verify that the Gila Trout genome is composed of 28 chromosomes, of which, 24 are metacentric and four are telocentric. Gila Trout maintains karyotypes of key chromosomal inversions observed in ancestral salmonids. Annotation and comparison of genes involved in adaptive immunity in the Gila Trout genome against other salmonids reveals conservation of coding regions but high variability within the introns and non-coding regions around the genes that could bolster immunocompetence in the face of novel pathogens.</p> Conclusion <p>This genome provides a key resource for the further monitoring and conservation of the Gila Trout.</p>