The most recent review of the genus Gompholobium Sm. (Fabaceae: Mirbelieae), published in 2008, considered Gompholobium nitidum Sol. ex Benth. to exhibit a high degree of variation, ranging from very compact shrubs with linear leaflets, to open shrubs of a taller stature with lanceolate leaflets, through to dense shrubs with oblong leaflets with obtuse-emarginate apices. We use morphological and ddRAD sequencing data to recognise three species from this broad complex, linked with topographic and edaphic complexity in the study area (Laura south to the Atherton Tablelands, north-east Queensland): (1) G. nitidum sens. strict. is a narrowly distributed taxon limited to the white sands of coastal dunes north of Cooktown, with a single disjunct population south of Cooktown; (2) a novel species described here, G. cinctum M.T.Mathieson & C.L.Simmons, has a slightly broader distribution across the skeletal sandy loams of sandstone formations in the Cooktown region; and (3) G. papuanum Merr. & L.M.Perry, previously subsumed into G. nitidum, is reinstated and occurs broadly across north-east Queensland in woodlands from west of Townsville to Cape York, the Torres Strait Islands and into Papua New Guinea.