Over the last decade, there has been increasing circumstantial evidence for the action of natural selection in the genome, arising largely from molecular genetic surveys of large numbers of markers. In nonmodel organisms without densely mapped markers, a frequently used method is to identify loci that have unusually high or low levels of genetic differentiation, or low genetic diversity relative to other populations. The paper by Mäkinen et al. (2008a) in this issue of Molecular Ecology reports the results of a survey of microsatellite allele frequencies at more than 100 loci in seven populations of the three-spined stickleback (Gasterosteus aculeatus). They show that a microsatellite locus and two indel markers located within the intron of the Eda gene, known to control the number of lateral plates in the stickleback (Fig. 1), tend to be much more highly genetically differentiated than other loci, a finding that is consistent with the action of local selection. They identify a further two independent candidates for local selection, and, most intriguingly, they further suggest that up to 15% of their loci may provide evidence of balancing selection.