<p>Population size estimation is critical for determining sustainable harvest levels of hunted species. Spatial capture-recapture via non-invasive genetic sampling is one method employed to estimate population size and is especially useful in habitats where aerial surveys are not possible. Developments in DNA sequencing technologies have led to the application of amplicon-based genotyping-in-thousands by sequencing (GTseq) for genotyping tissue and non-invasive genetic samples. Here we developed and assessed the power of a GTseq single nucleotide polymorphism (SNP) panel for individual identification. We performed population structure and diversity analysis of Sitka black-tailed deer (<i>Odocoileus hemionus sitkensis</i>) tissue samples from native and transplanted populations in Alaska and British Columbia. We then demonstrated that we could perform individual matching on fecal pellet samples from central Southeast Alaska (CSEAK). Our panel contains 248 SNPs and has enough power for individual identification with as few as 30 loci across all sampled populations. We identified population structure aligned with island geography and translocation histories. To select panel SNPs, we sampled our initial genomic data from one island in CSEAK, resulting in ascertainment bias when applying the panel outside of CSEAK. We highlight that this ascertainment bias led to lower locus variability in populations other than CSEAK. For individual identification outside of CSEAK, we recommend subsetting the panel to only use loci that are variable for the population being studied. If intending to estimate patterns of diversity and differentiation across populations outside of CSEAK, we recommend re-designing the panel with additional range wide genomic data.</p>