Open-pollinated seeds were assayed for allozyme polymorphisms at 24 loci to estimate genetic diversity and assess multilocus associations in 16 populations of Cunninghamia lanceolate (Lamb.) Hook in People’s Republic of China. On average, percentage of polymorphic loci was 88. 00, number of al-leles per locus was 3. 00, and expected heterozygosity was 0. 394. Distribution of genetic diversity was random but allele frequency at seven loci correlated with geographic and climatic variables. Six percent of total gene diversity was attributed to among-population differentiation; 94% resided withinpopulations. Two-locus gametic disequilibria were found in 15 of 16 populations and highter order ga-metic disequilibria were significant in most populations. Correlations between gametic disequilibria andgeographic and climatic variables were random. Results suggested founde effect, population subdivision , occurrence across diverse environments and historical events from 2000 years of cultivation were factors in the generation and maintenance of genetic diversity and structure in this conifer.