Population structure of the important commercial brown shrimp, Crangon crangon, was investigated in samples from five UK sites using a multidisciplinary approach based on morphometrics, allozyme electrophoresis and amplified fragment length polymorphism (AFLP). Multivariate analysis of the morphometric data revealed variation in the tail shape of C. crangon from Wansbeck (north-east England), which was found to have longer inner uropod and telson lengths in comparison with all other sites. Linear discriminant analysis was also able to place 86% of the Wansbeck individuals in the correct group. Crangon crangon were screened at two allozyme loci (Gpi and Pgm) revealing higher levels of polymorphism at both loci than previously reported. Allozyme allele frequencies showed evidence of population subdivision between east and west coast UK sites (FST=0.011). Data from three AFLP loci (Cra47, Cra56 and Cra70) confirmed population differentiation (FST=0.083) and combined allozyme and AFLP genetic data identified C. crangon from Wansbeck as different from all other sites. Random genetic drift and selection in populations with restricted gene flow are likely to be the main causes of the differentiation observed. The results do not support an earlier report of six distinct populations based solely on morphometric analysis.