Abstract: This paper introduces four fields of molecular ecology studied in plant. These include phylogeography, alien species, conservation genetics and contamination. Molecular markers, used in phylogeographical studies, help find the refugia of species during last glaciation and its migration routes after glaciation; The succ essful establishment of alien species may attribute to hybridization with and introgression from native species; Then the importance of conservation genetics is discussed from four aspects; Finally, the possible contamination in molecular ecology studies including the ecological impacts of transgenic species is mentioned. 