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A great diversity of animal species adapted to life in the semi-arid Caatinga of northeastern Brazil, including seasonal killifishes, has been reported in the last three decades. More recently, field and molecular data have shown a high occurrence of ciyptic species. The killifish group herein analysed, the Hypsolebias magnificus species complex, is endemic to the middle and southern portion of the Caatinga, occupying about 120 km along the floodplains of the middle Sao Francisco River and some adjacent tributaries. Species of this complex are rare and presently considered threatened with extinction, being uniquely found in pools protected by trees and bushes. Single-locus delimitation methods were used to test species limits of populations displaying different colour patterns along the whole distribution of the complex. All analyses consistently supported the three nominal species and two new, herein described: H. gardneri Costa, sp. n., from the floodplains of the middle Sao Francisco River and H. hamadryades Costa, sp. n., from the Gorotuba River floodplains. The phylogenctic analysis highly supports H. hamadryads as sister to a clade comprising H. gardneri and H. harmonicus. Our field observations suggest that H. hamadryades is a miniature species. This study indicates that the H. magnificus complex comprises cryptic species apparently endemic to small areas and extremely vulnerable to environmental changes, deseiving high concern.