Lactococcosis is a disease of concern for aquatic animal health, affecting commercially and ecologically valuable species across freshwater and marine systems worldwide. Control of the disease is hindered by limited options for treatment and prevention, conflated by a lack of information on the three etiologic agents – Lactococcus petauri, L. garvieae, and L. formosensis. Historical misidentification has obscured the individual contributions of these closely related species to global disease, but preliminary studies indicate they have important differences in host-specific pathogenesis and immunogenicity relevant to disease management. To better understand the genetic background underlying these characteristics, we used comparative genomics to identify putative species-specific and shared virulence factors between the lactococcosis-causing bacteria (LCB). Twenty-four isolates of L. petauri (n=14), L. garvieae (n=6) and L. formosensis (n= 4) from aquatic and terrestrial clinical cases in the US and Canada were submitted for pangenome analysis in EDGAR 3.2. Dispensable genomes were screened for potential determinants of host virulence between the species and strains. The core genome was evaluated for shared virulence factors that could be targeted for cross-protective vaccine design. Conservation was confirmed for genes of interest in an expanded sample set by nucleotide and amino acid alignments against a custom database populated by all publicly available LCB genomes. Subcellular location and antigenicity of proteins with 100% conservation and high homology were predicted using UniProt and VaxiJen, respectively. We identified several species-specific genes of interest, and at least six well conserved virulence factors that are promising targets for further exploration.