Abstract: Conservation genetics deals with the genetic factors that affect extinction risk and genetic management regimes required to minimize these risks. In this review, we introduce the advance from the genetic diversity study and the influence of genetic diversity on ecosystem. Until now, most of conservation genetic studies still adopt selective neutral genetic markers, which generate a large amount of valuable information for conservation theory and practice. Two important implications of conservation genetics are introduced: (1) the identification of individuals, genetic unit or species, which is very important for conservation strategy making and efficiency improving; and (2) cryptic bottleneck caused by reproduction and dispersal limitation, which is often neglected in conservation practice. Generally, neutral genetic markers may not provide enough information for the genetic basis of species adaptation. In recent years, along with the development of ge-nomics, more and more studies begin to investigate the genetic basis of adaptation by using adaptive genetic markers. Limited by lack of the functional gene information, most of these studies adopt the genome scan-ning approach. The development of landscape genetics promotes the understanding of the neglected relation-ship between genetic diversity and the landscape heterogeneity. In addition to the genetic diversity study it-self, some studies found that plant genetic diversity may influence the ecosystem structure and function. This illustrates that genetic diversity in both endangered species and common species can play an important role to ecosystem integrity and sustainability. Finally, we briefly discuss how to integrate the genetic diversity into conservation practice more effectively. And, we also indicate the gap between Chinese and international ad-vanced studies at the area of conservation genetics.