Peru has globally important elasmobranch fisheries, and mobulids are no exception. However, little is known about Peru’s small-scale mobulid fisheries. Mismatches between fishing reports and studies regarding species occurrence suggest a problem in identification methodologies of mobulids at the species level. This is supported by evidence of external resemblance between species, landings of incomplete bodies, and the use of a single name for the five species known to occur in Peruvian waters (“Manta” for Mobula birostris, Mobula munkiana, Mobula mobular, Mobula tarapacana and Mobula thurstoni). Given the need for improved conservation and management measures of mobulids in Peru, we tested the applicability of DNA barcoding combined with morphological identification to better understand mobulid catches by small-scale fisheries in north Peru. A total of 137 samples of muscle tissue from mobulids captured during fishing activities were collected of which 99 amplified and analysed for Cytochrome C Oxidase Subunit I (COI). Samples of the five species known to occur in Peru were obtained, confirming captures of all of them by local fisheries. Morphological identification allowed us to correctly identify more than 94% of specimens to the species level even though most of them arrived butchered (e.g., only pectoral fins). Increased capacity building and training for morphological identification of mobulid species by field observers, authorities, and fishermen, combined with molecular tools, is highly recommended to avoid mistakes in landings reports and to correctly enforce conservation measures for these species.