Arabidopsis thaliana has been used as a model plant for molecular genetics studies. Recently, Arabidopsis has been utilized in an increasing number of ecological and evolutionary studies. These studies are beginning to explain three “black boxes” of ecology: the nature of the mutations responsible for phenotypic variation, female–male interactions in the pistil, and the genetic basis of speciation. Among the advances are the inclusive fitness of haploid gametophytes, the testing of the arms-race model, morphological diversity, and reproductive isolation. Important methods include quantitative trait locus (QTL) mapping and molecular population genetics. Most significantly, natural variations of various aspects are now available via the taxonomic revision of its closely related species, and by the worldwide collection of accessions. Some conspicuous works using maize, Drosophila, and other species will be also discussed.