Release of captive bred individuals into the wild is now a conservation management approach to increase the depleted natural wildlife populations. Such method has been initiated for conservation of wild fish population on Qinghai Tibetan Plateau (QTP), a region of high level of species endemism. Platypharodon extremus is an endemic schizothoracine fish species and a dominated species in the plateau water ecosystem of the QTP in the past, it is now enlisted as an endangered species. However, phylogenetic and genetic information have not been previously considered in the ongoing stock enhancement program. In this study, genetic and demographic processes of the populations across the distribution of this species were assessed, using the mitochondrial DNA control region and Cyt-b.We found that all populations displayed low nucleotide diversity suggesting severe historical bottleneck events and high haplotype diversity indicating recent population expansion. Both the phylogenetic tree and the minimum spanning tree showed no significant genealogical structures corresponding to sampling locations. Population histories including bottleneck, exponential expansion and the absence of population structure indicate that demographic processes highly influenced genetic variation within and among populations of P. extreums. The data presented is consistent with a historical bottleneck and recent population expansion for all four populations based on several complementary analyses of the genetic data and inferred from demographic history (0.26 to 0.36 Mya). This genetic variation and demographic processes should become the baseline information for evaluating genetic effects of stock enhancement program and ongoing conservation decision making.