The study of species boundaries in areas of sympatry provides important insight into speciation processes. We investigated whether (i) two sympatric holothurians, Holothuria scabra and H. s. var. versicolor constituted species, and (ii) specimens of intermediate phenotype hybrids. Results from allozyme and 16S mtDNA sequence analyses indicated these two sea cucumbers to be distinct but young biological and phylogenetic species.