The giant gartersnake is a federally threatened species endemic to California’s Central Valley that has responded to habitat loss by utilizing irrigation canals and fields associated with rice agriculture, as well as mitigated wetland habitats. Color polymorphisms of melanin and stripe coloration in giant gartersnakes vary across subpopulations; however, the underlying genes controlling coloration are currently unknown. We are interested in examining the genetic underpinnings of color variation in giant gartersnakes because these polymorphisms may be under selection in these different habitat types. We will sequence the Mc1r gene in the giant gartersnake, as it has been associated with melanin levels in other reptile species. Additionally, we will perform restriction site-associated DNA sequencing using the restriction enzyme PstI which makes cuts roughly every 4 kilobases, allowing for greater representation of the genome, and a genome-wide association analysis to look for single nucleotide polymorphisms correlated with melanism and stripe coloration. Stripe color in giant gartersnakes appears to be continuously distributed, therefore genetic influence will likely be mediated by multiple loci. There is growing evidence that genetic mechanisms controlling color polymorphism correlate to other ecological traits, which may be especially interesting when examining the differences in color morphs across increasingly isolated subpopulations.