Neptunia Lour. (Fabaceae) is a mimosoid genus of 22 species that occur worldwide in the tropics and subtropics and is the sole mimosoid genus with aquatic species, the pantropical N. oleracea and N. plena. The genus is characterized by unarmed prostrate or ascending stems, thigmonastic leaves, and heteromorphic inflorescences with distally perfect but proximally sterile or male flowers. Previous molecular studies reconstructed Neptunia as monophyletic from three chloroplast regions and nrDNA markers, but were unable to resolve inter- and infraspecific relationships. We applied a target-capture approach with the Angiosperms353 bait-set to sequence hundreds of nuclear genes and the chloroplast genome to infer species relationships of the 22 Neptunia species. DNA sequences were reassembled with HybPiper, gene trees were reconstructed with maximum likelihood, and the nuclear species tree was estimated in Astral III. Phylogenies estimated with the Angiosperms353 bait-set were more resolved than previous studies based on Sanger sequencing data. The reconstructed phylogeny identified clades of species that correlated to their geography, in particular an American clade and an Australian clade. The two aquatic species were sister to each other, indicating a single transition into an aquatic habitat. Species boundaries did not correspond to clades for some species, such as N. plena, but others formed a monophyletic group.  Relationships among species and supporting morphological characters will be discussed for taxonomic considerations, with a focus on the aquatic, American, and Australian clades.