These .alleles files derive from data analysis in pyRAD_v.2.15 (Eaton 2014). pyRAD analyses were performed using the following parameters: ‘Minimum coverage for a cluster’ 10; ‘Clustering threshold’ 0.95; ‘Minimum samples in a final locus’ was adjusted according to the number of individuals in the given population; 'Number of individuals with shared heterozygote sites’ 60 %; ‘Ns in a consensus sequence’ 110; ‘Heterozygote sites in a consensus sequence’ 3; ‘Max number of SNPs in a final locus’ 10; ‘Max stack size’ 30; ‘Hierarchical cluster groups’ were specified for each species according to populations. The .alleles files give as output the individual loci and indicate variable sites (*: phylogenetically informative sites, -: singletons). For each locus it provides the sequence data for each sample and indicates the location of variable sites. The two alleles in an individual are printed out for each sample at each locus. For more informatio refer to pyRAD_v.2.15 manual (Eaton 2014) We provide an .alleles file for each of seven species of the spider genus Stegodyphus (family Eresidae): Stegodyphus lineatus Stegodyphus mimosarum Stegodyphus africanus Stegodyphus dumicola Stegodyphus tentoriicola Stegodyphus sarasinorum Stegodyphus pacificus