Genetic analysis of the four Trisopterus (Gadidae) taxa suggests that the interrelationships of the two morphs of poor cod (T. minutus minutus in the Atlantic and T. minutus capelanus in the Mediterranean) should be reconsidered. The Mediterranean poor cod T. m. capelanus is more closely related to bib T. luscus than to the Atlantic poor cod, so the population structure in the Atlantic and Mediterranean poor cod must be considered separately. Among 635 Atlantic individuals there was some evidence of poor cod population differentiation (allele frequency heterogeneity test Pc0·0005; F ST =0·0135, Pc0·0005). Levels of genetic variation were similar to those reported for related gadoid species. Some differentiation was present on the Norwegian coast (samples from Trondheimsfjord) and between the Faeroe Islands (Faeroe Bank) and the adjacent European coastal location. In contrast no statistically significant population differentiation was evident in Mediterranean poor cod, but fewer samples and individuals were screened. 2000 The Fisheries Society of the British Isles