Largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game and domesticated fish. Here a high-quality chromosome-level reference genome of a female M. salmoides was produced by combining Illumina, PacBio and Hi-C sequencing, aiming to better understand the evolution of traits such as pathogen resistance and environmental adaptations. The genome size was 844.88 Mb with a contig N50 of 15.68 Mb, and 23 chromosomes anchoring 99.9% of the genome sequences. A total of 26,370 protein-coding genes from 3415 gene families, of which 127 unique to M. salmoides. Mining of publicly available RNA-Seq sequences from healthy M salmoides identified sequences of known fish viral pathogens whose apparent tolerance could be linked to the expansion of 91 immune-related gene families providing high resistance to disease. The prevalence of such expressed viral elements captured in the M. salmoides transcriptome suggests an history of interaction between the fish and the viral environment. The high-quality genome will be a fundamental resource to understand M. salmoides traits that enable the successful colonization of novel and changing environments across the world.