This dataset contains data from 645,337 single nucleotide polymorphisms (SNPs) that were genotyped on GenoChip 2+ microarrays. The SNP data were ascertained from the mtDNA, Y-chromosome and autosomes for each individual, depending on their biological sex. In total, 5,205 mtDNA and 10,272 Y-chromosome SNPs were extracted from the array data. These data files have been uploaded as .csv files and also be uploaded as plink-formatted files. Details about the analysis of the SNP data can be found in the associated manuscript: Theodore G Schurr, Ramaz Shengelia, Michel Shamoon-Pour, David Chitanava, Shorena Laliashvili, Irma Laliashvili, Redate Kibret, Yanu Kume-Kangkolo, Irakli Akhvlediani, Lia Bitadze, Iain Mathieson, Aram Yardumian, Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus), Genome Biology and Evolution, 2023; evad198, https://doi.org/10.1093/gbe/evad198