Members of the Hypsolebias antenori species group comprise a diverse clade of morphologically similar seasonal killifishes occurring in a vast region of the semi-arid savannah of northeastern Brazil. The present paper focuses on an assemblage of three allopatric cryptic species (H. antenori from isolated coastal river drainages, Hypsolebias igneus from the São Francisco River basin and Hypsolebias coamazonicus sp. nov. from the Parnaíba River basin) sharing almost identical colour patterns, including the presence of an orangish red anal fin in males, thus herein named as the red-finned assemblage. A tree-based approach using mt-DNA (cytochrome b) supports delimitation of all three species, but indicates that the red-finned assemblage is paraphyletic – H. igneus and H. coamazonicus are closely related to Hypsolebias nudiorbitatus, whereas H. antenori is the sister group to a clade comprising all 13 species of the H. antenori group included in the analysis. Morphological characters are useful to diagnose species, but are not informative for most clades highly supported by molecular data. H. coamazonicus is distinguished from all other congeners by the possession of a dark grey or black stripe on the dorsal fin in males. The basal position of H. antenori is related to uplift episodes involving the Araripe-Borborema plateau during the Miocene, which isolated the coastal area inhabited by H. antenori from the remaining areas of the Caatinga. The sister group relationship between H. igneus and H. coamazonicus is attributed to a past connection between the São Francisco and Paranaíba River until the Tertiary.