To investigate the genetic diversity， phylogenetic relationships， and genetic differences between the northern subspecies （BFL） and “YOULU No.3” strain of largemouth bass， this study analyzed the genetic diversity of both populations. A total of 20 individuals from the BFL and 20 from the “YOULU No. 3” strain were selected for whole-genome sequencing. Genetic diversity was assessed by comparing observed heterozygosity （H_o）， expected heterozygosity （H_e）， polymorphism information content （PIC）， and nucleotide diversity （P_i） between the two populations. Phylogenetic relationships and genetic structure were explored through a phylogenetic tree， relationship matrix， principal component analysis （PCA）， linkage disequilibrium decay curves， and Admixture analysis. Additionally， a selection scan based on population differentiation index （F_ST） and P_i was conducted to identify selected genes， followed by Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analysis. The results showed that the H_o， H_e， and PIC values for the two populations were 0.329， 0.344， 0.276 for the BFL and 0.327， 0.342， 0.275 for “YOULU No.3，” with no significant differences （P>0.05）. However， the P_i value of the BFL was significantly higher than that of “YOULU No.3” （P<0.01）. Phylogenetic trees， relationship matrices， PCA， and admixture analysis revealed that the two populations belong to different subgroups. Linkage disequilibrium decay analysis indicated that the BFL exhibited faster decay than “YOULU No.3”. Selection scan results showed strong selection signals on chromosomes 5，6，7，14，22， and 23 in “YOULU No.3” GO and KEGG enrichment analysis suggested that genes related to feeding and immunity were under selection during the domestication and breeding of “YOULU No.3”. This study indicates that the BFL and “YOULU No.3” come from different subgroups， with the BFL exhibiting higher genetic diversity and “YOULU No.3” undergoing stronger selection pressures， mainly related to feeding and immunity. The findings provide support for the conservation and genetic improvement of largemouth bass resources.