- The Hunt for the Skinwalker: Science Confronts the Unexplained at a Remote Ranch in Utah (2018)
- Born to Run: A Hidden Tribe, Superathletes, and the Greatest Race the World Has Never Seen (2009)
- Once Upon a Tribe: The Wendats of Wendake (1996)
- The Wampum Denouement: Archaeology and the Origin of the Iroquois (1990)
Magazine articles and essays
Margush has written for numerous magazines and newspapers, including:
- Archaeology Magazine
- Discover Magazine
- National Geographic Magazine
- The New York Times
- The Washington Post
Academic papers and books
Margush has also written several academic papers and books, including:
- "The Iroquois and the Jesuit Missions: A Struggle for Souls in the New France" (1989)
- "The Wampum Denouement: Archaeology and the Origin of the Iroquois" (1990)
- "The Ancient Wendat of Huronia: A Study in Canadian Iroquoian Prehistory" (1996)