A new species of Swartzia section Terminales—S. neglecta—is described from the threatened Chocó-Darién biodiversity hotspot of western Colombia. Distinction of the species from close relatives is based on morphological diagnosability and geographical range cohesion, as revealed by analysis of data obtained from herbarium specimens. Swartzia neglecta is distinctive in bearing prominent villous to lanate indumentum on the filaments of the two larger stamens, among other features. It is also notable for the time elapsed between its first collection in 1857 and its publication in this work. A preliminary conservation status assessment employing the IUCN Red List threat categories and criteria suggests that S. neglectashould be categorized as Near Threatened.