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Abstract BackgroundPathogenicLeptospiraspecies are globally important zoonotic pathogens capable of infecting a wide range of host species. In marine mammals, reports ofLeptospirahave predominantly been in pinnipeds, with isolated reports of infections in cetaceans. Case presentationOn 28 June 2021, a 150.5 cm long female, short-beaked common dolphin (Delphinus delphis delphis) stranded alive on the coast of southern California and subsequently died. Gross necropsy revealed multifocal cortical pallor within the reniculi of the kidney, and lymphoplasmacytic tubulointerstitial nephritis was observed histologically. Immunohistochemistry confirmedLeptospirainfection, and PCR followed bylfb1gene amplicon sequencing suggested that the infecting organism wasL.kirschneri. LeptospiraDNA capture and enrichment allowed for whole-genome sequencing to be conducted. Phylogenetic analyses confirmed the causative agent was a previously undescribed, divergent lineage ofL.kirschneri. ConclusionsWe report the first detection of pathogenicLeptospirain a short-beaked common dolphin, and the first detection in any cetacean in the northeastern Pacific Ocean. Renal lesions were consistent with leptospirosis in other host species, including marine mammals, and were the most significant lesions detected overall, suggesting leptospirosis as the likely cause of death. We identified the cause of the infection asL.kirschneri, a species detected only once before in a marine mammal – a northern elephant seal (Mirounga angustirostris) of the northeastern Pacific. These findings raise questions about the mechanism of transmission, given the obligate marine lifestyle of cetaceans (in contrast to pinnipeds, which spend time on land) and the commonly accepted view thatLeptospiraare quickly killed by salt water. They also raise important questions regarding the source of infection, and whether it arose from transmission among marine mammals or from terrestrial-to-marine spillover. Moving forward, surveillance and sampling must be expanded to better understand the extent to whichLeptospirainfections occur in the marine ecosystem and possible epidemiological linkages between and among marine and terrestrial host species. GeneratingLeptospiragenomes from different host species will yield crucial information about possible transmission links, and our study highlights the power of new techniques such as DNA enrichment to illuminate the complex ecology of this important zoonotic pathogen.