The tropical barnacle Tetraclita forms a belt on hard substrates in the intertidal zone of the Red Sea. Based on morphological data, three distinct species were suggested to exist, occupying different vertical levels — T. barnesorum, T. rufotincta and T. achituvi. In this study we used molecular (12S mitochondrial ribosomal DNA) and ecological data to examine whether this morphological variability reflects genetic differences, or is a result of environmental factors. Adults and spats, collected from settlement plates, were censused and screened genotypically using single strand conformation polymorphism (SSCP) analysis, and settlement dynamics was recorded. We provide evidence for the existence of only two distinct species, and point out both phenotypic plasticity and convergence within and between the proposed species. Cyprids of T. achituvi settle specifically at the lower part of the Tetraclita belt, and feature one phenotype. In contrast, T. rufotincta, occupying the upper and middle portions of the Tetraclita belt, settles throughout the range, shows phenotypic plasticity (three variants), and presumably undergoes selection at the lower part. Thus, the vertical zonation of Tetraclita is produced by the combination of pre-settlement and post-settlement factors, in T. achituvi and T. rufotincta, respectively. The examined system may offer a model in which to study the mechanisms underlying sympatric speciation.