Populations of two varieties of Botryllus niger from three points along the southeastern coast of Brazil were compared genetically, in order to evaluate their taxonomic status. Variety giganteum, (two colour morphs, orange and grey) and var. niger were analysed for 25 enzyme systems by starch gel electrophoresis, of which nine gave reproducible results. The levels of gene variation observed were high in all populations of var. niger analysed (H = 0.239), but only moderate (H = 0.112) in the populations of var. giganteum. This may reflect observed differences in the population sizes of the two varieties. The gene identity obtained for pairwise comparisons between populations or colour morphs of the same variety was at the lower end of the range normally associated with conspecific populations (I = 0.76-0.98). In contrast, a high level of gene differentiation was observed between the two varieties (I = 0.404), with five out of 12 loci being diagnostic of each one. Since the two supposed varieties live sympatrically, this indicates that they are reproductively isolated, and therefore deserve specific status. The varietal names are thus raised here to specific level, as Botryllus niger and Botryllus giganteum.
