Abstract: Genetic diversity, aims to reveal the variation in DNA sequence within species, is an important component of biodiversity. Maintain genetic diversity is recognized as one of the main goals of 2010 and 2020 CBD (Convention on Biological Diversity) because genetic diversity facilitates species adaptation and ecosystem function. In addition, it is suggested that genetic diversity monitoring and conservation should be listed as the action target in 2030 CBD. However, much of the study on population genetics or genetic diversity remained in academic area with little application in practical conservation management. Generally, despite influenced by biological and ecological factors, overexploitation of natural resources and/or habitat fragmentation might reduce genetic diversity, increase genetic differentiation and limit gene flow among populations and further influenced the integrity and authenticity of ecosystems. In this study I reviewed the genetic diversity focused on the China′s critical endangered tree species since 1996 to date (238 studies, 150 endangered tree species). I found a high proportion (38%) of genetic studies had applied on endangered tree species but with few of the results applied to conservation management. Recently national parks have been listed as protected areas in China′s official documents to protect the authenticity and integrity of natural ecosystems. Facing the great opportunity and challenges, I suggested monitoring and conservation of genetic diversity should be considered as the fundamental for the establishment and development of the national park in China. In addition, DNA based genetic diversity monitoring and important genetic factors such as effective population size should be strengthened as recommend by other international conservation policy.