Environmental DNA (eDNA) has become a powerful tool for assessing biodiversity in different environments and may be a complementary method compared to traditional methods to assess biodiversity. We tested eDNA as a complementary tool to assess marine biodiversity at Lobos de Afuera islands (ILA) in Peru. Nine water samples were collected from three sites within ILA using a commercial eDNA kit and then analyzed using vertebrate, teleost, and marine mammal primers targeting the 12S rRNA gene. Operational taxonomic units (OTUs) classified at order, family, genus, and species levels were compared to baseline reports obtained through visual survey methods. Compared with traditional methods, eDNA assays identified 26% fewer species. However, it was a cost-effective method due to the higher number of identified bony fish species per sampling unit. The eDNA assays provided a broader representation of higher taxonomic levels (order, family, and genus), with a higher sensitivity for bony fish than the traditional methods used. Also, the same numbers of orders and families reported by visual assessments were detected with eDNA. Our study shows practical implications for using eDNA for biota assessments in remote and isolated areas. Future efforts should aim to catalog the biodiversity from inaccessible places using eDNA-methods.