Leptospirosis is a zoonosis with ubiquitous distribution caused by spirochetes belonging to the genus Leptospira sp., endemic mainly in tropical and subtropical regions of the world and capable of infecting domestic animals, free-living animals, and humans. Although well documented in terrestrial animals and humans, little information is available on its distribution and impact on marine animals. There are few studies assessing cetaceans’ health status, and even scarcer are those focused on leptospirosis research. In this context, considering the One Health approach, the present study aimed to investigate the occurrence of pathogenic Leptospira sp. in cetaceans on the Brazilian coast. Kidneys of 142 cetaceans belonging to 19 species were collected. DNA was extracted, and the diagnosis was performed by LipL32-polymerase chain reaction. Genetic characterization was conducted based on secY gene sequencing. Pathogenic Leptospira sp. DNA was detected in 14.8% (21/142) of the tested cetaceans, with coastal species presenting a significantly higher frequency (p-value = 0.03) of infected individuals (25%, 17/68) than oceanic species (7.5%, 4/53). It was possible to amplify and sequence three strains (one for Sotalia guianensis, one for Stenella clymene, and one for Pontoporia blainvillei), all of them identified as Leptospira interrogans, with high similarity with sequences from Icterohaemorrhagiae serogroup. Phylogenetic analysis revealed sequences from the present study grouped in species-specific unique clusters but very close to pinnipeds in the same area, evidencing the presence of two distinct haplotypes circulating on marine mammals in the region. We could demonstrate that cetaceans can act as carriers of pathogenic leptospires. Moreover, the proximity with anthropogenic areas could play an important role in leptospirosis’ dynamics of transmission in a One Health context.