Identification of horses at high risk for developing laminitis, such as those predisposed to Equine Metabolic Syndrome (EMS), is an essential component of any equine management strategy. Pro-opiomelanocortin (POMC) and melanocortin 4-receptor (MC4R) are two genes expressed in neurons of the hypothalamus that are involved in the regulation of energy homeostasis in mammalian species. Re-sequencing of these two genes revealed a total of five synonymous SNPS; one in MC4R and four in POMC. The MC4R SNP showed an association with body condition score (BCS) and a significant association with light and dark shades of coat color. Three of the POMC SNPs were located in coding regions. All three were synonymous. The last POMC SNP was located upstream of the coding region of the gene, and is potentially regulatory. Horses were genotyped for the MC4R SNP using Fluorescence Resonance Energy Transfer (FRET) technology and melting curve analysis. New sequence data was generated for POMC and four distinct haplotypes were identified within the gene. Comparisons between the protein sequences of the two equine genes and other mammalian species show a high amount of evolutionary conservation. Additional work should focus on elucidating the exact nature of the link between the MC4R SNP and coat color, gathering data on more horses to determine if there is statistical significance between the MC4R SNP and BCS, as well as work to determine if the regulatory mutation in POMC affects transcript copy number in the hypothalamus. Either gene could affect adiposity in the horse, which is a known risk factor for both EMS and laminitis.