The Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM) convened in Olhãu, Portugal 7–9 May 2014. Members met to discuss and consider the five Terms of Reference (ToR) decided by the ICES Science Committee. The report contains the main issues discussed and the management recommendations for each of these ToRs. Dorte Bekkevold (Denmark) chaired the meeting, which opened at 09:00 on the 7 May and closed at 13.30 on 9 May. The meeting had 23 participants representing the European Joint Research Centre in Italy and 12 other member nations (Belgium, Canada, Denmark, France, Germany, Iceland, Norway, Portugal, Russian Federation, Spain, Sweden and UK). WGAGFM have established a three-year term for the chair, and it was the final year for the current chair’s term. The members present at the meeting unanimously supported that WG member Professor Gary R. Carvalho be-come the next Chair for WGAGFM. Members discussed the current status and way forward in integrating genomic meth-ods with marine fisheries management. Fisheries biologists and managers have long acknowledged the importance of intraspecific diversity, as described for most ex-ploited species, though management remains mostly based at the scale of large sea basins with fixed administrative boundaries and rectangular management areas. The latter geographically defined framework typically fails to match the biological struc-ture of populations. It follows that in order to move towards sustainable fisheries, a central challenge is to incorporate spatial biological diversity into contemporary man-agement schemes Moreover, population connectivity and dynamics must be reliably monitored to support management strategy implementation. Genomic methods pro-vide one important tool to achieve this goal and members discussed cases incorporat-ing such approaches with other relevant data in diverse fisheries management scenarios, showing that evolutionary thinking can add valuable information to the suc-cessful implementation of strategies to promote profitable and sustainable fisheries within an ecosystem context .Members found that the examples demonstrate the meth-ods’ relevance for a suite of management questions and recommend that ICES SCICOM and ACOM push for more standardized use of the methods as well as initiate that application of genetic methods are included in its training courses. WGAGFM received an advice request from OSPAR (4/2014) on “Interactions be-tween wild and captive fish stocks”. WGAGFM contributed information on genetic effects and potential management solutions to mitigate adverse impact. Several studies have demonstrated that the gene pools of wild populations change when hatchery produced farm fish escape (or are released) at large-scales. Several studies also report that intro-gression by escaped farm fish can incur a fitness cost to wild populations, causing in-creasing concern for the continuing health and viability of wild populations and awareness about conserving native fish gene pools. Knowledge is mainly based on salmonids fish but should be transferrable to fully marine organisms, making aquacul-ture escapees a general concern. Molecular quantification has proved valuable for demonstrating introgression by farm fish. However, WGAGFM reviewed studies and found that in many cases, the introgression process is complex, e.g. with respect to escape rates and genetic make-up of escapees, and impacts can therefore be difficult to assess and predict. Members concluded that in order to develop and implement relia-ble management strategies and advice, locally and internationally, it is of importance to consider on a case-by-case basis the different options for the analysis of genetic data to quantify level of introgression. Following on from work initiated in 2013, members discussed the application of ge-netic methods in shellfish. Invertebrates such as shellfish of interest in an aquaculture context have very different life histories compared to finfish and these characteristics mean that the transfer of technology and selection approaches from the finfish industry to the shellfish one is not always simple or even possible. However, this emphatically does not mean that the general principle of identifying adaptive markers and utilizing them in the scenarios outlined above cannot result in benefits to both industry and wild populations. Recent developments in genetic screening techniques (e.g. Next-Genera-tion Sequencing and genome sequencing) promise even greater power to identify markers linked to traits of interest and the incorporation of such techniques should be encouraged in the shellfish aquaculture context.