Ethnic issues in Guatemala are commonly analyzed using theoretical frameworks that underscore the role of Maya activism in promoting Mayan identification. However, these frameworks often pay insufficient attention to the local significance of phenotype. In this study, I propose an alternative framework to explain ethno-racial status in contexts of mestizaje. Based on this framework, I investigate whether phenotype, captured by skin color, is a significant dimension of ethno-racial status in Guatemala using nationally representative survey data and regression analysis. I specifically examine the association between skin color and ethnic self-identification, and differences by ethno-racial characteristics in the perception of skin color discrimination and in the desire for a whiter skin color. I find evidence of a direct association between skin color and ladino self-identification, evidence of a greater perception of skin color discrimination by individuals with more indigenous characteristics, and evidence of a direct association between indigenous ancestry, captured by indigenous first language, and the desire for a whiter skin color. These findings reveal the significance of phenotype as a distinct dimension of ethno-racial status in Guatemala beyond ancestry and ethnic self-identification.