The spotted turtle (Clemmys guttata) is a widespread semi-aquatic species found in shallow wetlands across eastern North America. Despite its broad range, populations have declined by more than 50% due to habitat loss and poaching. To develop conservation genomics resources for the species, we produced an annotated, chromosome-level reference genome using a combination of long- and ultra-long read data. The assembly is 2,286,936,868 base pairs, 98.5% of which are assembled in 25 contigs, which is consistent with published karyotypic data. In addition, 16 of these contigs represent gapless, telomere-to-telomere chromosome sequences. BUSCO scores indicate a highly complete assembly (99.4%), and annotation yielded 21,335 protein-coding genes, which BUSCO scores indicate are also highly complete (98.4%).