Dedicated ichthyological surveys in four active karstic caves in the Mexican state of Chiapas (Grijalva River drainage basin) resulted in the discovery of the same number of hypogean populations of Rhamdia catfishes assignable to two different species: R. laticauda and R. guatemalensis. The taxonomic identity of these populations was initially determined based on morphological traits and subsequently corroborated with molecular data in a phylogenetic framework. For the most part, these newly discovered populations exhibit partial and variable troglomorphism (vs. fixed), a pattern that has been observed in most other cave-dwelling species/populations of Mexican Rhamdia, and possibly caused by gene flow with and/or incipient speciation from epigean lineages. Since most hypogean forms of Mexican Rhamdia derive from/are part of a larger R. laticauda clade, our discovery of cave-dwelling populations assignable to R. guatemalensis is noteworthy and includes the very first record of a R. guatemalensis population with pronounced and widespread troglomorphism. Our discovery of hitherto unrecorded populations of hypogean Rhamdia highlights the continued importance of exploration in the process of documenting subterranean biodiversity, particularly in regions of the world rich with cave systems. Our findings corroborate the notion that, among Neotropical fishes, the catfish genus Rhamdia is one of the most prone and effective at colonizing subterranean habitats and establishing viable hypogean populations.