Cryptic biodiversity continues to be revealed worldwide, even in apparently well-known groups such as carnivorans. The Neotropical Otter (Lontra longicaudis) presents shape variation in its nose pad, a character that has been used to differentiate species in this group. Based on this, 3 subspecies are recognized: L. l. annectens (Mexico, Central America, and South America west of the Andes), L. l. enudris (Amazon and Orinoco basins), and L. l. longicaudis (Paraná basin and remaining distribution). Previous studies partially supported their distinctness based on mitochondrial DNA markers, morphometrics, and ecological niche modeling. We analyzed genome-wide nuclear markers (ultraconserved elements) of 29 L. longicaudis individuals across the species’ range to assess its population structure. Phylogenomic analysis recovered L. longicaudis as paraphyletic with robust support, with 1 clade comprising samples from Mexico and Colombia (trans-Andean populations) and another encompassing the remaining samples (cis-Andean populations), which grouped with 2 other South American species, L. felina and L. provocax. Principal component and admixture analyses strongly differentiated the 2 main L. longicaudis groups, and distinguished the Amazonian individuals from the remaining cis-Andean samples. Our results support the recognition of trans-Andean populations of L. longicaudis as a distinct otter species, which should be recognized as Lontra annectens.

The neotropical otter (Lontra longicaudis) is associated with freshwater systems and is generally found at elevations lower than 1500 masl. Its diet is based on fish and crustaceans. We present 3 photorecords of the neotropical otter at the divide between 2 hydrological basins in the Sierra de Manantlán Biosphere Reserve, Jalisco, México. The photos were taken at an altitude near 2000 masl, and one of them was >600 m from a water source. The area does not present optimal conditions for the presence of otter since water flows are low, fish are absent, and crustaceans are scarce. These records are evidence of the neotropical otter at high altitude in environments where conditions are suboptimal for the species. In addition, the importance of conserving the basin headwaters is discussed, since the headwaters can support movement or occasional stays of the neotropical otter in marginal habitat and thereby maintain the connectivity between basins and facilitate genetic exchange between otter populations.