Dedicated ichthyological surveys in two karstic caves in Costa Rica resulted in the discovery of hypogean populations from three epigean species of catfishes of the genus Rhamdia. The taxonomic identity of these populations was initially determined based on morphological traits and subsequently corroborated with comparative DNA sequence data in a phylogenetic framework. Individuals from all hypogean populations documented herein exhibit only partial troglomorphism, characterized by only moderate (vs. complete) integumentary depigmentation without extreme eye reduction/loss. A similar pattern of incomplete troglomorphism at the individual level has been observed in other cave-dwelling species/populations of Middle American Rhamdia, and tentatively attributed to gene flow with and/or incipient speciation from epigean lineages. Since most hypogean forms of Rhamdia derive from/are part of a larger clade of primarily R. laticauda, our discovery of cave-dwelling populations assignable to R. nicaraguensis and R. guatemalensis is noteworthy, particularly in the case of the former, which represents the first taxonomically verified record of a cave-dwelling population of this epigean species. Among our findings is the remarkable discovery of hypogean populations from two different species of Rhamdia (R. laticauda and R. nicaraguensis) inhabiting the same cave (Gabinarraca). This finding is particularly significant because it represents the first time that cave-dwelling populations from different species of Rhamdia are reported to be living in syntopy. Continued discovery of cave-dwelling populations during targeted ichthyological surveys reinforces the notion that our understanding of the diversity of hypogean Rhamdia is incomplete and that sustained exploration and taxonomically sound documentation work are paramount to advancing knowledge about the diversity and evolution of these group of Neotropical catfishes.