The genetic diversity and structure of six Korean populations of Taxus cuspidata Sieb. et Zucc., a widespread and dioecious tree native to east Asia, was examined. Although Korean populations are isolated and located over 1000 m a.s.l., they maintain moderate levels of allozyme variation (average percent of loci polymorphic = 45%, mean number of alleles per locus = 1.78, mean expected heterozygosity = 0.192) compared to species with similar life history and ecological traits. In addition, Korean populations harbour slightly higher levels of genetic diversity than populations of T. breuifolia Nutt. in the western United States and Canada. A considerable, high level of heterozygote deficiency was observed in Korean populations of T. cuspidata (mean FIS = 0.299). Although significant heterogeneity in allele frequency were detected between populations at all 12 polymorphic loci (p < 0.01 at Per-2 and p < 0.001 at others), among-population genetic differentiation accounted for 5.6% of the total variation. Indirect estimates of the number of migrants per generation (Nm) (4.22, calculated from GST; 6.02, calculated from the mean frequency of four private alleles) indicate that gene flow is extensive among Korean populations of T. cuspidata. It is suggested that factors such as obligatory outcrossing (dioecious plant), high fecundity, long generation times, ability to regenerate by stump sprouting, and occasional seed dispersal by birds may contribute to the moderate levels of genetic diversity within populations and low allozyme divergence among populations of T. cuspidata.