The Portuguese sole, Synaptura lusitanica Capello, 1868, is distributed from Portugal to Angola. In Portugal, it occurs on the west coast and on the south-eastern coast. The genetic and morphological variation of S. lusitanica was studied based on protein electrophoresis and morphometric and meristic analyses of samples collected in four areas along the Portuguese coast. The genetic analysis was based on 12 loci, 10 of which were polymorphic. The morphological analysis included 12 morphometric measurements and 7 meristic counts. Both analyses indicated divergence between the west coast sample (Setúbal) and the other samples collected in the south-eastern coast (Olhão, Tavira and Vila Real de Santo António). Although the discreteness of the west coast individuals of S. lusitanica was not completely evident, a conservative approach to the fisheries management of this species would consider two independent stocks.