Among Taiwanese endangered woody species, populations of Bretschneidera sinensis have distributed around the widest natural geographic area in northern Taiwan. However, they occupy as small patches with isolated tuft tree stands in the fragmented forests. In this study, genetic structure of B. sinensis from five subpopulations are examined using isozyme techniques. The results indicated that the degree of among population differentiation was high (F_(ST) = 0.256). This value reveals that nearly 75 % of the detected genetic variation resides within populations. Selection imposed by habitat variation and the effect of restricted gene flow (Nm = 0.727) to be the causes of high F_(ST). Excessive homozygote deviated from Hardy-Weinberg expectation (F_(IS) = 0.226) may be referred to Wahlund effect. Results of pollination experiment show that B. sinensis is a insect-pollinated outcrossing species. The potential influences of mating type, natural selection, gene flow, genetic drift and the Wahlund effect on genetic differentiation within and among populations of B. sinensis are discussed. Management practices and genetic conservation of this species are proposed.