Molecular genetic data have found widespread application in the identification of population and conservation units for aquatic species. However, integration of genetic information into actual management has been slow, and explicit and quantitative inclusion of genetic data into fisheries models is rare. In part, this reflects the inherent difficulty in using genetic markers to draw inferences about demographic independence, which is generally the information of the greatest short-term interest to fishery managers. However, practical management constraints, institutional structures and communication issues have also contributed to the lack of integration. This paper identifies some of the organizational, conceptual and technical barriers that have hampered full use of genetics data in stock assessment and hence fishery management and outlines how such use could be enhanced.