The relative importance of natural selection in the diversification of organisms can be assessed indirectly using matrix correspondence. The present study determines the environmental and genetic correlates of microgeographical variation in the growth form, leaf form and flower morphology in populations of four Aeonium species from section Leuconium using partial regression methods. The phylogeny of the four species and the other 12 species in the section was deduced from amplified fragment length polymorphism (AFLP). Pubescence of floral organs and flower size correlate with the phylogeny while traits related to growth form, leaf form, flower construction and inflorescence size correlate with ecological factors. The variation in the latter four traits may therefore reflect selection by current ecological conditions while variation in pubescence and flower size may reflect historical events like neutral mutations, founder events and drift. Additionally, the morphological analyses revealed a large amount of variation in all traits within populations. This suggests a possible influence of microhabitat on the variation in morphology of Aeonium in the Canary Islands.