Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We show that DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. DNAm patterns are further compared between hatchling blood cells and embryonic gonads undergoing TSD.