Monitoring genetic parameters is important for setting effective conservation and management strategies, particularly for small, fragmented, and isolated populations. Small populations face increased rates of genetic drift and inbreeding, which increase extinction risk especially when gene flow is limited. Here, we applied a Genotyping-in-Thousands by sequencing (GT-seq) panel to inform recovery action for the northern Idaho ground squirrel (Urocitellus brunneus), listed as threatened under the U.S. Endangered Species Act. We evaluated genetic diversity, structure, connectivity, and effective population size to address species recovery goals. We delineated 15 conservation units: (1) three evolutionarily significant units that represent long-term population structure and evolutionary history, (2) nine management units that reflect current demographic connectivity and restrictions to gene flow, and (3) three adaptive units that capture adaptive differentiation across the species range. Effective population sizes per management unit were small overall (mean 38.16, range 2.3-220.9), indicating that recovery goals have not been reached. Our results suggest that connectivity within evolutionarily significant units should be maintained through the restoration of dispersal corridors. We recommend further sampling of subpopulations that harbor unique adaptive differentiation and that are geographically isolated to refine our understanding of adaptive variation. We recommend ongoing genetic monitoring with the same GT-seq marker panel to detect dispersal, assess effective population size, monitor the effects of inbreeding, and evaluate adaptive differentiation to monitor the effects of management action and environmental change. This study provides an illustration of how genetic and genomic tools can inform management and assess recovery goals for a threatened species.