Rhys Jones met his wife, Jo, a graphic designer, while working at the BBC. He has described their first meeting by saying "The day we met, I was semi naked and she was throwing water over me." The couple have two children, and live between homes in London (previously in Islington, now in a Grade I listed house in London's Fitzrovia in the West End) and Holbrook in Suffolk. Rhys Jones owned "Undina", the , fifty-year-old wooden sailing yacht which was used in "Three Men in Another Boat"; he spent £500,000 on her restoration and in 2013 stated she was for sale for £195,000, "probably less".