His wife, Akemi, whom Shimomura met at Nagasaki University, is also an organic chemist and was a partner in his research activities. Their son, Tsutomu Shimomura, is a computer security expert who was involved in the arrest of Kevin Mitnick. Their daughter, Sachi Shimomura, is director of Undergraduate Studies for the English Department at Virginia Commonwealth University and the author of Odd Bodies and Visible Ends in Medieval Literature.