Between the 16th and 19th centuries, over 12 million people were kidnapped mainly in West and West Central Africa and transported to the Americas during the trans Atlantic slave trade. Despite having received 200,000 Africans during the slave trade, no study in Mexico has focused on the characterization of the African genetic ancestry of its Afro-descendant population. In this study we worked together with Afro-Mexican communities to characterize their genetic ancestry using dense genome-wide genotyping. The dataset consists of 380 self-identified Afro-descendants, indigenous and mestizo population from three Mexican states. Additionally, we collected genealogical, self-identification and phenotype data such as skin pigmentation, height, weight, hip to waist ratio and hemoglobin. Genotype data revealed that up to 46% of the genetic ancestry of some individuals is of African origin, with the remaining being mainly of indigenous origin. We are currently exploring local ancestry and admixture patterns in this population as well as correlations between the genetic ancestry, self-identification and phenotypes; and have identified trends of public health relevance. For example, we observed significantly higher prevalence of overweight and obesity among women from Afro-Mexican communities, when compared to the national mean and to neighboring indigenous and mestizo populations. Interestingly, we have also noticed that individuals who self-identify using labels that reflect the color of their skin (e.g. negro, moreno) tend to have higher levels of African ancestry than individuals who use the term “Afro” (e.g. Afro-Mexican, Afro-descendant, etc) for self-identification. Lastly, since Afro-Mexicans currently suffer from poverty, discrimination, lack of recognition as a vulnerable minority, and limited access to health services, this study contributes to their appreciation as part of Mexico’s mosaic of diversity and will hopefully set the stage for health interventions to abate the obesity epidemic in the sampled regions.