Wilshusen earned his doctorate at the University of Colorado in 1991. He has thirty-five years of experience as a field archaeologist, professor, curator, and contractor. He has worked for universities, cultural resource management (CRM) firms, state and federal government, and tribes. Wilshusen is best known for his research on the Neolithic demographic transition, early Pueblo village formation, Southwestern migration pathways, early great house communities, and Navajo ethnogenesis.