Alien invasive species can cause huge economic loss in agricultural and forestry production, and threaten biodiversity and human health. The research of invasion ecology is of significance in understanding the invasion mechanisms of alien invasive species and in developing corresponding sustainable control methods. Molecular marker is regarded as a useful tool in approaching some essential issues in the research of invasion ecology. In this paper, the applications of molecular marker techniques in the studies of identification, geographic distribution, invasive source, spread pattern, genetic variation, hybridization, and gene introgression of alien invasive species were reviewed, and the application prospects were discussed.