The processes underlying divergent selection and genetic adaptation have been on the evolutionary biologists agenda for a long time. In this study we used the three-spined stickleback (Gasterosteus aculeatus) study system, a perfect system to study the evolution of similar traits in different lineages exposed to similar environmental conditions. Lind and Grahn (2011) have found directional selection caused by pulp mill effluent on populations of three-spined stickleback along the Swedish coast. In their study, they identified 21 AFLP- outlier loci indicated to be under selection. Here we converted some of these anonymous AFLP loci into sequenced markers and aligned them to the stickleback genome. Four out of five loci, aligned within or close to coding regions, on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the locus, located on chromosome VIII, have been identified to be under selection for fresh water adaption in other studies, including Baltic Sea stickleback populations (Mäkinen et al. 2008a,b). We believe that this is feasibly method that can be used as a starting point for identification of genes and genomic regions possible involved in adaptation, both for model and non-model organisms.