A high concentration of endemic species of seasonal killifishes has been recorded for a small area encompassing the highland plateaus associated with the upper section of the Carnaúba de Dentro River drainage and adjacent drainages of the middle section of the São Francisco River basin, northeastern Brazil. The present study is primarily directed to the taxonomy of theH.fulminantisspecies complex in this region, and describes habitat decline and extirpation of natural killifish populations recorded in field studies between 1993 and 2017. Both morphological characters and molecular species delimitation methods using single-locus models (GMYC and bPTP) support recognition of two closely related endemic species,H.fulminantisandH.splendissimusCosta,sp. n.The new species is distinguished from other congeners of theH.fulminantiscomplex by having a red pectoral fin in males, well-developed filamentous rays on the tips of the dorsal and anal fins in adult males, and the second proximal radial of the dorsal fin between the neural spines of the 8thand 9thvertebrae in males. Most recent field inventories indicated possible local extinction of populations ofH.fulminantisandH.splendissimusin the studied area, but additional field studies should be made in other parts of the upper Carnaíba de Dentro River basin to evaluate the current conservation status of these species.