Natural selection has been theoretically and empirically proven to alter patterns of linkage disequilibrium (LD). Reciprocally, recombination, the driving force behind LD, modifies the signature of natural selection by reintroducing variation in a punctuate manner across the genome. To date, efforts to identify genes that have been subjected to historical selective pressure by examining polymorphic variation and allelic association have frequently fallen short of unambiguously distinguishing selection from other biological mechanisms. Contemporary genetic maps that describe LD in fine detail represent a much needed tool that can be exploited by researchers aiming to tease apart these opposing signals.