Neptunia windleriana, a new polyploid species of the pantropical genus Neptunia, is described and illustrated. This plant is endemic to the state of Bahia, Brazil, and is found in areas of Caatinga near the São Francisco River. Among the species occurring in Brazil, it is most similar to N. plena, a widespread species, by having a gland on the petiole, but it differs mainly by the number of pairs of pinnae and leaflets, shape of the spike in bud, and the size of the peduncles. It is morphologically distinct from all other species of the genus by the combination of prostrate subshrub habit, smaller leaves, shorter petiole and shorter rachis length, few-flowered, globose spikes, 10 stamens, and glabrous ovary. The presence of monocrystals in the bundle sheath cells of the bracts of N. windleriana is recorded here for the first time for the genus, together with the chromosome number (2n = 56 vs. 2n = 28, ∼52, 54, 56, 72, 78 for three other species of the genus occurring in Brazil), it can be also used to identify the species. The epidermis of the stipules, leaflet, and bracts of N. windleriana is uniseriate, with paracytic stomata. The vascular system has collateral arrangement with the vascular bundles covered by a sheath, with or without isolated monocrystals. Our data support earlier hypotheses that Neptunia has a base number of x₂ = 14 which seems to be a secondary basic number that originated from an ancestral stock with x₁ = 7 and underwent karyotypic evolution by polyploidy. A key to the Brazilian species of Neptunia as well as anatomical, cytogenetic, taxonomic, and geographic distribution data, ilustrations and photos are provided.