Upon graduating from West Point, Lyon was commissioned as a 2nd lieutenant and assigned to the 2nd U.S. Infantry regiment after graduation and served with them in the Seminole Wars and the Mexican-American War.
After the Mexican War, Lyon was then posted to the frontier, where he participated in the massacre of Pomo Native Americans at Clear Lake, California, the 1850 "Bloody Island Massacre";[REF] as many as 100 old men, women and children were killed.