Abstract The unique endemic cave fauna of the Maros karst cave system (Sulawesi, Indonesia) includes atyid freshwater shrimps only known from their species descriptions. An extensive survey revealed a total of ten species in epigean and subterranean rivers: Two non-endemic, four species endemic to Sulawesi (genus Caridina) and four stygobiont species (genus Caridina, Marosina, and Parisia) only endemic to the Maros karst. A molecular phylogeny revealed (1) two independent colonizations of Sulawesi’s Maros karst caves by species of Caridina (Clade 1) derived from endemic ancestors, and (2) an exclusively stygobiont group (Clade 2, Marosina, Parisia) possibly derived from an amphidromous, anchialine cave-dweller. Our approach revealed another cryptic cave species of Caridina and challenges the taxonomic status of four Sulawesi endemics. In conclusion, the freshwater shrimps of the Maros karst are a challenging but rewarding group that can contribute to our understanding of the evolution of cave-dwelling species and atyid phylogenetics.