We provide a number of data files associated with the article "Genetic structure and effective population size of Sydney rock oysters in eastern Australia" (DOI: 10.1007/s10592-021-01343-4). These include: - VCF file generated following the SNP calling methods in the article. File contains genotype information for the primary sample set (n=363), filtered to retain biallelic SNPs with <25% missing data (75,231 SNPs). - Sample metadata, containing site ID, individual ID, and the latitude & longitude of sampling location. - Main script used to generate data and conduct analyses described in the article. - Zip folder containing files associated with demographic modelling using moments Other relevant data can be found in the Electronic Supplementary Material for the article.