Recent studies have implicated beta-hemolytic streptococci as opportunistic pathogens of marine mammals, including southern sea otters (Enhydra lutris nereis), but little is known about their prevalence or pathophysiology. Herein, we focus on risk factors for sea otter infection by a single beta-hemolytic streptococcal species, Streptococcus phocae. Streptococcus phocae was first identified as a marine mammal pathogen in 1994, and the first report in southern sea otters was in 2009. Its broad host range encompasses fish, pinnipeds, cetaceans, and mustelids, with S. phocae now recognized as an important pathogen of marine species worldwide. We assessed risk factors and lesion patterns for S. phocae infection in southern sea otters. Using archival necropsy data, S. phocae prevalence was 40.5% in fresh dead otters examined 2004–10. Skin trauma of any type was identified as a significant risk factor for S. phocae infection. The risk of infection was similar regardless of the cause and relative severity of skin trauma, including mating or fight wounds, shark bite, and anthropogenic trauma. Streptococcus phocae–infected sea otters were also more likely to present with abscesses or bacterial septicemia. Our findings highlight the importance of S. phocae as an opportunistic pathogen of sea otters and suggest that the most likely portal of entry is damaged skin. Even tiny skin breaks appear to facilitate bacterial colonization, invasion, abscess formation, and systemic spread. Our data provide important insights for management and care of marine species.