Abstract: The phenomenon ‘somaclonal variation’ refers to genetic and/or epigenetic changes in cells or regeneration that arise through the culture of plant cells, tissues and organs. Some genetic bases underlye the plant somaclonal variation, which can be integratively determined and identified at morphological, cytological, biochemical and molecular biological levels. Plant somaclonalvariation is one of available resources in plant breeding, but it is an unw elcome puzzle to be won through in plant micropropagation in vitro and genetic transformation. This paper reviews the progress in study of the genes is and identification of plants omaclonal variation at both cytological level and molecular biological level, and discusses the problems and prospects of applying somaclonal variation in breeding and improving plant varieties.