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Abstract Listrura is a genus of small pencil catfishes of Trichomycteridae that currently comprises 12 valid species in coastal drainages of Southern and Southeastern Brazil, all with fossorial dwelling habitats and eel-like morphology. Here, we describe a new species of Listrura known from only two specimens collected in an interval of 24 years in order to make it taxonomically available for biodiversity inventories and conservation decisions. The new species is morphologically distinguished from its congeners by the combination of features, as pectoral-fin rays counts, number of free vertebrae, number caudal-fin procurrent rays, interopercular odontodes counts and the anterior-most position of dorsal and anal fin. Partial sequences of the mitochondrial gene cox1 were used to infer the phylogenetic relationships and biogeography of the new species and its congeners. The new species is the first freshwater fish endemic to a continental island in the Atlantic Forest Biome, and only the second trichomycterid endemic of an island.