The molecular mechanisms underlying organismal fitness in complex environments is just beginning to be illuminated. One of the pre-eminent model systems that span the molecular to field fitness chasm is the natural variation in glucosinolate defence metabolites within the Capparales. In this system, there have been extensive surveys of variation in the same phenotypes across a breadth of species and the molecular basis of the major polymorphisms both within and between species is largely known. This is showing an extensive array of evolutionary processes that create and recreate specific polymorphisms and traits that is highly similar both within and between species. Further, early field trials with single gene recreations of natural variation are showing that selection is highly fluctuating both from site to site and from year to year within a location. This review goes into the specific ecological, evolutionary and molecular observations for each of the major loci controlling natural variation in glucosinolates.