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Biological invasions may cause serious damage to the native environments and threaten the native biodiversity. Molecular genetic approaches have been found to be powerful tools for investigating the ecological and evolutionary aspects of biological invasions because the genetic structure and level of genetic variation of an invasive species are changed following its invasion. The present article reviews the use of molecular markers in addressing various aspects of invasive species. The application of these techniques has shown that many invasive species are actually "cryptic" species - species whose uniqueness is only recognizable at the genetic level. An estimation of the actual number of invasive species is essential when evaluating its ecological and economic impacts. Molecular genetic approaches have also enabled the source populations of invasive species to be identified. Reconstructions of invasion histories are crucial to preventing future invasions and conserving the native biodiversity, while comparisons of genetic variations between the native and introduced populations provide valuable opportunities to elucidate the mechanisms of rapid adaptation demonstrated by many invasive species.