Value of the Data •Pedigree analysis of the Boer and Nubian goat breeds in Mexico assists stakeholders in monitoring the breeds' genetic diversity, and its outcome can be used to prevent significant loss of genetic diversity in breeding programs. •Monitoring the breeds' genetic diversity in a breeding program, through characterization of genetic structure and variability, may help maintain long-term genetic diversity and prevent genetic erosion and the presence of population bottlenecks. •Further, the data can be used to estimate other population parameters of genetic diversity for goats in Mexico, and to make other recommendations to maintain long-term genetic diversity and a sustainable genetic progress of these breeds.