Abstract:Bretschneidera sinensis Hemsl., with important research value, is an endangered species endemic in East and South Chin. We used inter-simple sequence repeat(ISSR) markers studied the genetic diversity within and among six populations of B.sinensis. The genetic diversity at species level was high(PPB: 75.70%; HES: 0.304 5; H: 0.450 1). However, relatively low genetic diversity existed within populations. Population in Minjiangyuan(MJY) exhibited the greatest level of variability(PPB: 60.13%; HEP: 0.238 1; H: 0.347 5), whereas the population in Baishanzu(BSZ) showed its own variability at the lowest level(PPB: 44.86%; HE: 0.173 6; H: 0.255 6). By the genetic analysis of the ISSRs, we revealed a relatively high level of genetic differentiation among populations by Nei’s gene diversity statistics(21.81%), Shannon’s information measure(22.79%) and analysis of molecular variance(AMOVA)(18.62%). The main factors responsible for the relatively high level of differentiation among populations were probably related to the predominant outcrossing reproductive system and recent habitat fragmentation, and a significant correlation was between genetic distance and geographic distance(r=0.626 7, P<0.05). The high diversity would hold promise for conservation and restoration efforts to save the endangered species from extinction.