Supplementary material for "Homogenization of populations in the wildflower Texas bluebonnet (Lupinus texensis)." Here we sample 187 individuals in 12 matched pairs of neighboring wild and seeded populations of the Texas bluebonnet (Lupinus texensis), a species popular in commercially available wildflower seed mixes used by both the Texas Department of Transportation and the public. We use genotyping by sequencing to identify 11,741 genome-wide single nucleotide polymorphisms, as well as a smaller number of SNPs from the chloroplast genome, to analyze population structure and genetic diversity within and between the populations. VCF file of total raw single nucleotide polymorphisms (SNPs) from 24 populations, produced from dDocent pipeline. These SNPs are unfiltered. De novo assembly of a reference catalogue and genotyping was performed with dDocent v2.2.6 (Puritz et al. 2014). dDocent combines several existing software packages into a single pipeline designed specifically for paired-end GBS/RAD data and takes advantage of both forward and reverse reads for SNP discovery.