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Skin cancer risk information based on melanocortin-1 receptor (MC1R) variants could inform prevention and screening recommendations for Hispanics, but limited evidence exists on the impact of MC1R variants in Hispanic populations. We studied Hispanic subjects, predominately of Puerto Rican heritage, from Tampa, Florida, US, and Ponce, PR. Blood or saliva samples were collected by prospective recruitment or retrieved from biobanks for genotyping of MC1R variants and ancestry informative markers. Participant demographic and self-reported phenotypic information was collected via biobank records or questionnaires. We determined associations of MC1R genetic risk categories and phenotypic variables and genetic ancestry. Over half of participants carried MC1R variants known to increase risk of skin cancer, and there was diversity in the observed variants across sample populations. Associations between MC1R genetic risk groups and some pigmentation characteristics were identified. Among Puerto Ricans, the proportion of participants carrying MC1R variants imparting elevated skin cancer risk was consistent across quartiles of European, African, and Native American genetic ancestry. These findings demonstrate that MC1R variants are important for pigmentation characteristics in Hispanics and that carriage of high risk MC1R alleles occurs even among Hispanics with stronger African or Native American genetic ancestry.