The threespine stickleback is a valuable organism for studying the molecular basis of adaptive evolution, as populations of these fish have adapted from marine to freshwater environments in many geographic locations. This publication of a reference genome and sequences of multiple marine and freshwater sticklebacks has enabled the genome-wide identification of regions of divergence between the populations; this will be a useful resource for studies of adaptation and ecological speciation. Insights that have already emerged include a substantial contribution of non-coding sequences to the divergent loci.