The dataset consists of genotypes (diploid base calls at variant sites) at 3,601 anonymous sites of the Arizona Toad (Anaxyrus microscaphus) nuclear genome. The genotyped samples are representative of the range of the species and its major population units, and the genotyped loci have a high degree of completeness. This data release consists of several files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All NCBI-derived accessions listed in the file can be searched at www.ncbi.nlm.nih.gov to retrieve sample and sequence information, as can the umbrella BioProject accession PRJNA995169 2. genotypes.genepop.txt, which contains inferred genetic variants in a common and convertible text-based format