Amphipholis squamata is considered to be the only echinoderm distributed worldwide, excepted in polar regions. This vast distribution area contrasts with a low dispersal potential due to the lack of a pelagic larval stage and an aggregative spatial distribution. Previous works have shown strong inter- and intra-population variability among adult individuals for both phenotype and genotype, although the species seems to be anatomically uniform. The aim of this work was to understand these individual variations at three different levels: (a) the morphological differences characterized by the colour of arms and disc; (b) the physiological variations estimated by luminous capabilities and (c) the genetic variations as revealed by RAPDs. Four populations were sampled in the system of Oliveri-Tindari in Sicily which consists of several lagoons completely isolated from the open sea and from each other for various periods. This system constitutes a suitable model for studying differentiation between closely neighbouring demes. Our results confirm that each colour variety possesses its own luminous capabilities; they also indicate that colour varieties are genetically differentiated