The diversity and ecology of meiofauna in caves is largely unknown. Therefore, we studied one anchialine and five freshwater caves in November 2014 and January 2016 in western Cuba. We recorded 10 invertebrate taxa with the most abundant being: Nematoda, Ostracoda, Acari and Copepoda. The meiofauna communities in the caves were relatively impoverished probably due to the combination of oligotrophic conditions and limited colonization by organisms from outside. We found 28 nematode taxa of which 23 never have been previously reported inhabiting caves. The previously exclusive marine genera Desmodora and Paralongicyatholaimus were reported for the first time in freshwater environments. Ironus cf. ignavus was the most abundant species in agreement with studies elsewhere. In freshwater caves, water runoff and organism dispersal from the surface likely determines the colonization of the sediment. Parthenogenetic and predatory/omnivore nematodes dominated in the studied caves probably due to the physical isolation and oligotrophy in the underground systems.