Polymorphism at six microsatellite loci was used to study genetic variability and population structure in six geographically distant natural populations of European hake (Merluccius merluccius L.). Four hundred and eighty-three individuals were sampled from Trondheimsfjord in Norway, the Celtic Sea, the southern Bay of Biscay, Faro off Portugal, the Mediterranean Sea north of the coast of Tunisia and the Adriatic Sea. Population subdivision was found between Mediterranean and Atlantic samples, θ = 0.029 (P < 0.001). No substructuring was found between samples within the Mediterranean Sea, θ = 0.003 and RST = 0.007 (P > 0.05). The Atlantic population structure appears to be more complex than previously suggested by the placement of stock boundaries by the International Council for the Exploration of the Seas (ICES). Analyses based on various models of microsatellite evolution all suggest that differentiation exists between Bay of Biscay and Portugese samples, θ = 0.013 (P < 0.001), RST = 0.036 (P < 0.001) which are currently managed as one stock. By contrast, fixation indices indicated no differentiation between southern Bay of Biscay samples and Celtic Sea samples, θ = 0.003 (P = 0.02), φST = 0.007 (P = 0.10) which are managed as separate stocks. These results suggest that if the observed trends are stable through time, current management policy of European hake may need revision.