The crucifer Arabidopsis thaliana has been the subject of intense research into molecular and developmental genetics. One of the consequences of having this wealth of physiological and molecular data available, is that ecologists and evolutionary biologists have begun to incorporate this model system into their studies. Current research on A. thaliana and its close relatives ably illustrates the potential for synergy between mechanistic and organismal biology. On the one hand, mechanistically oriented research can be placed in an historical context, which takes into account the particular phylogenetic history and ecology of these species. This helps us to make sense of redundancies, anomalies and sub-optimalities that would otherwise be difficult to interpret. On the other hand, ecologists and evolutionary biologists now have the opportunity to investigate the physiological and molecular basis for the phenotypic changes they observe. This provides new insight into the mechanisms that influence evolutionary change.