The miniature seasonal killifishSpectrolebiascostae, first described for the middle Araguaia River basin, has been also recorded from two areas in the middle Tocantins River basin, from where male specimens exhibit some differences in their colour pattern. Analyses directed to species delineation (GMYC and bPTP), using a fragment of the mitochondrial gene COI, strongly support two species,S.costaefrom the Araguaia River basin and a new species from the Tocantins River basin.Spectrolebiasgracilissp. n.is described on the basis of specimens collected from two localities separated by about 530 km, Canabrava River floodplains near Alvorada do Tocantins and Tocantins River floodplains near Palmeirante. Field inventories were unsuccessful in finding additional populations in the region, which is attributed to the high environmental degradation, including several large dams that have permanently inundated typical killifish habitats.Spectrolebiasgracilisis member of a clade also includingS.costae,S.inaequipinnatus, andS.semiocellatus, diagnosed by having the dorsal and anal fins in males with iridescent dots restricted to their basal portion, caudal fin in males hyaline, and caudal-fin base with two pairs of neuromasts. Within this clade, a single miniaturisation event is supported for the most recent common ancestor of the subclade comprisingS.costaeandS.gracilis, which differ from other congeners by reaching only about 20 mm standard length as maximum adult size.