<p>Whole genome resequencing can be a powerful tool for uncovering biological insights and quantifying population genomic metrics relevant to conservation. These insights have the potential to be most profound in secretive or elusive species that are understudied but whose populations may be waning. The western chicken turtle (<i>Deirochelys reticularia miaria</i>) is one such example where conservationists are concerned about reported population declines. Here, we report results from analyses of genome sequence data from western chicken turtles and how the associated inferences could be used to inform management decisions. We sequenced and assembled a novel reference genome, then conducted a population genomics resequencing survey across much of Texas that represents one of the first in any freshwater turtle. We uncovered fine-scale population structure indicative of natal philopatry. Absolute values of fixation indices were relatively small (all pairwise <i>F</i>_<i>ST</i><InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(\:\le\:\)</EquationSource> </InlineEquation>0.03), but principal component analyses of the resequencing data readily separated individuals into clusters that correspond to their geographic sampling sites (i.e., wetland mosaic) and phylogenomic analyses revealed monophyletic groupings that also correspond to wetland mosaic geography. Estimates of individual genome-wide heterozygosity (<i>H</i>) were similar to those observed for threatened or endangered turtle species. Collectively, our data suggest that western chicken turtle populations are spatially differentiated due to natal philopatry and limited gene flow. We discuss the relevance of these insights as they pertain to turtle biology, including the conservation implications of philopatry in a species of concern.</p>