In this study, we have examined the relative roles of gene flow and selection in determining population structure in the Atlantic cod, G. morhua, by comparing the patterns of variation at 10 polymorphic allozyme loci previously scored by MORK et al. (1985) to 1'7 cDNA- based nuclear restriction fragmentl ength polymorphisms (RFLPs) scored among 6 populations occupying similar geographic regions. If gene flow is responsible for the homogeneous population structure revealed by the allozymes, the nuclear RFLP loci are also expected to display low levels of population differentiation. If the RFLP loci exhibit significant heterogeneity among populations then gene flow can be eliminated as the explanation for the homogeneous allozyme patterns because gene flow is a process that affects all loci equally. By showing significant differences between the distribu- tions of RFLP and allozyme polymorphism among cod populations, our results discount the importance of gene flow and implicate a role for selection in affecting the distribution of protein variation in this species