Exostema (Rubiaceae) comprises 25 neotropical woody species, ranging from western South America and Mesoamerica to the West Indies, with 19 species occurring in Cuba and Hispaniola. Biogeographical hypotheses based upon a phylogenetic analysis of morphological data depict a South American origin for the group, with species radiations in the Greater Antilles. Molecular phylogenetic analyses were conducted using ITS and rbcL sequence data for a sample of 14 species of Exostema and nine species from eight closely related genera. Results indicate that Exostema is paraphyletic with respect to Coutarea, Erithalis, and Chiococca. Hypotheses invoking independent South American origins for subclades of Exostema are not supported. Coutarea and the South American Exostema species form a clade sister to the Caribbean Exostema species with terminal inflorescences. Relationships among axillary flowered Exostema species are not well resolved. Distribution, ecology, and seed traits indicate over-water dispersal is important for wide-spread species (e.g., E. caribaeum). Sister species relationships between the Cuban and Hispaniolan endemics E. salicifolium and E. acuminatum are strongly supported. Disjunctions between various regions of Cuba and Hispaniola are consistent with geohistorical connections between these composite islands. Biogeographical patterns found in Exostema are similar to those reported for other Caribbean plant groups, with vicariance detected in certain cases, and dispersal often indicated by distribution, ecology and phylogeny for many taxa.