Human-induced eutrophication is indirectly affecting aquatic organisms by altering their environment. This brings on altered selective pressures and could thereby cause changes in the genetic composition of exposed populations. Since anthropogenic environmental changes are usually occurring at a much higher rate than naturally occurring changes, they force populations to adapt to the new conditions faster than normal. Here, I have studied populations of three-spined sticklebacks (Gasterosteus aculeatus) from four eutrophicated and four adjacent reference sites, along the coast of Finland, to investigate if this species has responded genetically to the human-induced eutrophication of the Baltic Sea. For this purpose I used amplified fragment length polymorphism (AFLP) and found distinctions in genetic composition between the two habitats, as well as similarities between populations from eutrophicated sites. This suggests a similar genetic response to eutrophicated conditions by stickleback populations from different geographical areas. Moreover I found a distinct geographic structure among three-spined sticklebacks in the Baltic Sea.