Hypsolebia antenori is a seasonal killifish considered to be broadly distributed along the Caatingas basins of northeastern Brazil, with records in the coastal drainages of the rio Pacoti, rio Jaguaribe, crrego Virglio and rio Apodi-Mossor basins. Based on morphological characters and molecular phylogenetic reconstructions, it was possible to diagnose two new species and restrict H. antenori to the rio Jaguaribe basin. Hypsolebias gongobira new species is described from a temporary pool in the rio Pacoti basin in Cear State, in syntopy with the species threatened H. longignatus. Hypsolebias bonita new species occurs in the floodplains of the rio Apodi-Mossor basin and in the crrego Virglio microbasin in the Furna Feia National Park, in Rio Grande do Norte State. We also discuss the conservation status of these new species and how the So Francisco Interbasin Water transfer, and the agricultural and urban expansion in the semiarid may be adversely affecting these seasonal killifishes.