Evaluation the conservation strategies of endangered species based on population genetics Yu-Chung Chiang1 and Ya-Zhu Ko1 1 Department of Biological Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan In order to keep the critically endangered species away from risk of extinction, conservation managements designed for different species are an important strategy for the rare and endangered taxa. For examples, the perennial cycad, Cycas taitungensis Shen, Hill, Tsou & Chen and Amentoaxus formosana H. L. Li. are two endemic species with two and one remaining populations in Taiwan, respectively. For C. taitungensis, the IUCN was increased this endemic species to endangered level in 2009 caused by Aulacaspis yasumatsui, an invasive species that infests cycad plants in the past decade in Taiwan (IUCN Red List of Threatened Species, Version 2011.1: http://www.iucnredlist.org/). Populations have been in extreme decline and we need to enhance the conservation administration of the threatened taxa. For A. formosana, this species is categorized at the critically endangered level in the IUCN Red List of Threatened Species based on only population with thousands individuals. The Forestry Bureau in Taiwan has considered C. taitungensis and A. formosana for ex situ conservation management such as “seed storage” or “transplanting” to keep these endemic species survival if the wild population becomes extinct. Based on this propose, we estimate the genetic diversity, effective population size, and identify the distinct genetic units based on polymorphic microsatellite loci. We select individuals from different genetic units in order to maintain the maximum genetic diversity of C. taitungensis and A. formosana.