Sea lions (Zalophus) are highly susceptible to abscesses, which often accompany malnourishment and are a common secondary cause of mortality. The pathology of skin abscesses are complex and involve bacterial and fungal pathogens. Abscesses can persist and worsen without proper intervention, facilitating subsequent systemic infections. Previous studies have sought to identify pathogens that contribute to abscesses of various body sites (i.e., rectum and liver) among sea lions. However, little evidence exists on the bacterial and fungal microbiome profiles of skin abscesses. Moreover, since these studies have used traditional, arguably less-comprehensive PCR and culture techniques to measure the microbiome, limited evidence exists identifying the skin microbiome of abscesses in sea lions using next-generation sequencing (NGS). NGS offers a unique opportunity to better understand the microbial communities present in abscesses since all bacteria and fungi can be identified simultaneously, particularly down to the species level. This study characterized the core skin bacterial and fungal microbiome of 30 California sea lions (Zalophus californianus) with skin abscesses using NGS. Our findings revealed attributes of both bacterial and fungal dysbiosis and the co-occurrence of bacteria and fungi that may contribute to the development and persistence of skin abscesses. Clinically, this research underscores the need for NGS in diagnostics to address the complexities of abscess infections in marine mammals. Understanding the interplay between bacteria and fungi in these abscesses provides critical insights into more effective therapeutic interventions and can aid in the management of sea lion health in marine ecosystems.