Bacterial cultures of marine mammal samples often yield multiple genera and species, and it can be difficult to determine if a cultured bacterium is a primary pathogen or an incidental finding. To determine the relative risk of bacterial isolates among Atlantic bottlenose dolphins Tursiops truncatus at the United States Navy Marine Mammal Program (MMP), retrospective data on isolates cultured during June 1987 through June 2007 were organized into a novel, 5-tier risk categorization system limited to sole bacteria cultured from internal organ or fluid samples. Of 2586 bacterial isolates cultured, only 34 (1.3%) and 25 (1.0%) were sole isolates attributed to morbidity and mortality, respectively, and only 19 (0.7%) isolates were associated with mortalities without evidence of fungal or viral co-infections. Highest risk bacterial isolates were most likely to be identified in pleural fluid (33.3% of pleural fluid samples with bacterial isolates had only one genus), followed by renal (23.1%) and splenic (11.1%) tissue. Sole Staphylococcus aureus isolates were identified as the highest risk bacterial pathogens in the MMP dolphin population, accounting for 0.4 % of total bacterial isolates over a 20 yr period. In summary, isolation of sole bacterial isolates definitively associated with morbidity and mortality in marine mammals was uncommon in the MMP population. Our proposed risk categorization system may be useful in determining high risk pathogens among other marine mammal populations.