Vanilla claviculata, V. barbellata and V. dilloniana are distributed throughout the Caribbean islands and are all found in Puerto Rico. The vegetative parts of the species are similar; however, their conspicuous flowers easily distinguish them. Electrophoresis of seven polymorphic enzymes revealed that the genetic composition of the three species is also very similar: they deviate mainly from each other in allele frequencies rather than by specific alleles. A hierarchical analysis of genetic differentiation showed that the between-species component is slightly higher (FSG=0.237) than the component between populations within species (FPS=0.141). Nevertheless, they are efficiently recognized by their genotypic compositions. In V. barbellata and V. claviculata 97-99% of all individuals were assigned to the correct species. Assignment to a wrong species occurred only with individuals at localities where species coexist. This suggests that the species may hybridize.