The hemichordate Saccoglossus kowalevskii has been used as a developmental model to offer insights into the evolution of developmental mechanisms in deuterostomes, especially chordates. Along with echinoderms, they make up Ambulacraria, the sister clade to chordates. To date, most studies on S. kowalevskii have used a single population located near Woods Hole, Massachusetts. However, the species is known to occur from Maine to South Carolina. Very little is known about the genetic diversity of the Woods Hole population, and even less about diversity among other populations. Thus, to explore the diversity within and between the Woods Hole and other populations, we conducted population genomic analyses using data from whole genome sequencing. To do this, we collected 20 acorn worms at 4 sites (South Carolina, Virginia, Delaware, and Massachusetts), and sequenced whole genome DNA to ~20X coverage using paired-end Illumina Hi-Seq. There was little variation in our mapping success for whole genomes from all populations to the reference genome from Woods Hole. We characterized both the within and between population heterozygosity and tested for signals of geographic relatedness by analyzing FST, nucleotide diversity, and observed heterozygosity. We also investigated signals of isolation-by-distance and linkage disequilibrium. Because of the dependence of developmental projects on the Woods Hole population, we hope this study serves as a resource for the Saccoglossus community to determine if other populations are sufficiently genetically similar, and suitable, for EvoDevo and ecological research. We additionally hope this study helps clarify some questions about the natural history of S. kowalevskii by understanding their within species genetic diversity.