Plants of the genus Kobresia are alpine grass species of high ecological and economic importance. Vegetative growth is the dominant means of reproduction for the Kobresia. Studies suggest that substantial vegetative growth can reduce genetic diversity and renders populations less able to buffer changing and extreme conditions. Kobresia are dominant species in the Qinghai-Tibet plateau in China where they face harsh conditions and frequent disturbance. The genetic diversity of five Kobresia species (K. humilis, K. royleana, K. kansuensis , K. tibetica and K. setchwanensis) from the Qinghai-Tibet plateau was assessed. The results reveal high genetic diversity at the population level for all of the species and there does not appear to be a relationship between altitude and genetic diversity. AMOVA analysis shows that most genetic variability resides among individuals within populations, whereas only a minor portion is found among populations. Of the five species, K. royleana and K. kansuensis have the highest levels of gene flow and the lowest genetic differentiation. While K. setchwanensis has the lowest gene flow and the greatest genetic differentiation. The level of gene flow between populations and the mating system play a critical role in the genetic structure of these Kobresia populations. Despite the predominance of vegetative growth enough sexual reproduction occurs to maintain the relatively high genetic diversity in Kobresia populations.