The genus Xanthophytum (Rubiaceae) from Borneo, Java, the Philippines, New Guinea, and Fiji is revised. Thirty species are recognized. Twelve new species are described, viz. X. alopecurum, X. brookei, X. cylindricum, X. foliaceum, X. glabrum, X. grandiflorum, X. magnisepalum, X. minus, X. nitens, X. pubistylosum, X. sessile, and X. setosum. Two varieties have been raised to species, X. borneense (Valeton) Axelius and X. semiorbiculare (Bakh. f.) Axelius. A key, descriptions, typifications, illustrations and distribution maps are provided for all species. A hypothesis of the phylogenetic relationships is given, in the form of a cladogram, and discussed. An area cladogram for Xanthophytum and its biogeographic implications are presented as well as a new extended general area cladogram for the Indo-Pacific.