An enormous amount of naturally occurring genetic variation affecting development is found within wild and domesticated plant species. This diversity is presumably involved in plant adaptation to different natural environments or in human preferences. In addition, such intraspecific variation provides the basis for the evolution of plant development at larger evolutionary scales. Natural phenotypic differences are now amenable to genetic dissection up to the identification of causal DNA polymorphisms. Here we describe 30 genes and their functional nucleotide polymorphisms currently found as underlying allelic variation accounting for plant intraspecific developmental diversity. These studies provide molecular and cellular mechanisms that determine natural variation for quantitative and qualitative traits such as: fruit and seed morphology, colour and composition; flowering time; seedling emergence; plant architecture and inflorescence or flower morphology. Besides, analyses of flowering time variation within several distant species allow molecular comparisons between species, which are detecting homologous genes with partly different functions and unrelated genes with analogous functions. Thus, considerable gene function differences are being revealed also among species. Inspection of a catalogue of intraspecific nucleotide functional polymorphisms shows that transcriptional regulators are the main class of genes involved. Furthermore, barely more than half of the polymorphisms described are located in coding regions and affect protein structure, while the rest are regulatory changes altering gene expression. These limited analyses of intraspecific developmental variation support Doebley and Lukens's proposition (1998) that modifications in cis -regulatory regions of transcriptional regulators represent a predominant mode for the evolution of novel forms, but await more detailed studies in wild plant species.