As the field of genomics and human genetics continues to push our understanding of disease and biodiversity through an ever-increasing pool of genomic data, it is critical to consider the social, ethical, and legal implications of using such data. This is particularly true for genomic data pertaining to Indigenous Peoples, much of which has been collected and (re)used in research without the informed consent of Indigenous communities or without the return of benefits of research discoveries to these communities. Indigenous data sovereignty (IDSov) provides a framework through which Indigenous Peoples can assert their right to control data on or about their communities and lands. Here, we provide a review of IDSov and recommendations for how researchers can integrate it into their genomic research with Indigenous Peoples. Inclusion of IDSov in genomic research design supports meaningful partnerships between researchers and Indigenous communities, ensuring the maximization of benefits and minimization of harms for improved community health and prosperity.