A molecular genetic analysis of Coris julis from different sites in the Mediterranean and the Atlantic and C. atlantica from the Cabo Verde Islands was applied to infer phylogenetic relationships between the taxa. More precisely, partial 12S mitochondrial rDNA sequence data were used in maximum parsimony, neighbour-joining, and maximum likelihood analysis to generate phylogenetic trees. The polymorphism observed indicated an important differentiation between the C. atlantica and C. julis specimens and supported the existence of two different species.