Abstract: The birth of the journal of Molecular Ecology in 1992 symbolized the beginning of a new discipline, the molecular ecology. Earlier than that, many Chinese scientists who have involved in the study of genetic diversities had also initiated great interests in molecular ecology. This review provided progress in six aspects of studies that covered nearly all investigation areas in molecular ecology during the past ten pears. The main aspect of study was on population and conservation genetics that covered more than half of academic researches achieved in China. The plant species investigated included cultivated, wild and endangered plants. Study on phylogeography, speciation and hybridization and that on kinship, parentage and breeding system had been paid enough attention. In contrast, there were fewer studies on ecological genetics and molecular adaptation. Since the latter is the main interests of most ecologists and also a priority research topic of molecular ecology, it should be strengthened by intimate collaborations between ecologists and molecular biologists. Although there were quite a number of studies on ecological effects of genetically modified organisms (GMOs), yet their ecological nature was usually being ignored as there were fewer ecologists involved in such study at present. It was proposed that investigation on the interaction between GMOs/other organisms with known genetic characters and environment would probably unveil the gene (genome) function in respect to ecology and in turn would promote the advance of molecular ecology in theory.