Camellia oleifera, a hexaploid evergreen broadleaf shrub or small tree, is the dominant woody oilseed crop in China. Understanding the spatial pattern of genetic diversity in wild C. oleifera is essential for conservation and utilization of genetic resources. Six wild C. oleifera populations were sampled along a latitudinal gradient in subtropical evergreen broadleaf forests of Southern China. A new high-throughput sequencing-based microsatellite genotyping method was developed to resolve allele dosage uncertainty in hexaploid wild C. oleifera with 35 microsatellite markers. Finally, the dataset of mcrosatellite genotypes was generated with corrected allele dosages. In addition, another dataset of microsatellite genotypes with uncorrected allele dosages (showing only different alleles) was generated, for mimicking the situation of current microsatellite genotyping methods.