ABSTRACT. The Iguaçu River basin is a tributary to the upper Paraná River in southern Brazil, and is considered an important aquatic ecoregion that, although having few species of fish, 51-71% of these are apparently endemic. Ancistrus abilhoai is one of three recently described species for this basin and is currently considered endemic to the basin. In this study, we present the chromosomal structure of two populations of Ancistrus abilhoai one collected in the Iguaçu River, in Paraná State, and another collected in the Timbó River, a tributary of the Iguaçu River, in the State of Santa Catarina. Karyotype analyzes were performed in 11 specimens from the Iguaçu River (four females and seven males) and 12 specimens (all males) from Timbó River, revealing 2n = 48 chromosomes with a karyotype formula of 22m + 14sm + 6st + 6a in both populations. Analysis of active nucleolar organizer regions (Ag-NORs) and fluorescent in situ hybridization (FISH) with 18S rDNA probes revealed the submetacentric pair 13 bearing marks at terminal positions on the short arms. Considered as plesiomorphic chromosomal markers in Loricariidae, asynteny 18S and 5S rDNA, and small amounts of heterochromatin were observed. In this study, the first chromosomal data of A. abilhoai are presented with comments on karyotypic characteristics of the genus.