EM (expectation–maximization) algorithm procedures were used to estimate mating-system parameters in four natural populations of Thujaorientalis L. from China using seven allozyme marker loci (Fest1, Idh1, Idh2, Mr, Pgi2, Skdh1, and 6Pg2). The mean single-locus outcrossing rate was 0.70 for the species, but estimates showed that there was significant heterogeneity among loci within populations. Multilocus estimates of the outcrossing rate showed that there was significant heterogeneity among populations and among trees within populations. The mean multilocus outcrossing rate (0.75) was higher than the outcrossing rate (0.63) observed in a closely related conifer, Thujaoccidentalis L., but lower than estimates that have been reported for most other conifers. Significant heterozygote deficiencies, relative to Hardy–Weinberg and mating-system equilibria, were observed in all filial populations. In contrast, the maternal populations conformed to Hardy–Weinberg and mating-system equilibria at most loci. Self-fertilization and other forms of inbreeding (e.g., sibling mating) within the sampled populations are important contributors to the low outcrossing estimates in this conifer.