John Leng & Co, an investment subsidiary of the Dundee-based publisher, bought the puzzle publisher for an enterprise value of £85m.
Puzzler Media managing director Mel Lewis said: "Our new partnership with DC Thomson offers us an exciting opportunity to continue the successful development of Puzzler Media.
"We are now rapidly advancing our development in mobile phones, interactive TV and the internet with sudoku, opening exciting opportunities internationally with planned launches in India, Russia and USA."
Puzzler Media, which is based in Redhill with a staff of 60 and publishes titles such as Puzzler, Puzzler Collection and Puzzler Sudoku, was acquired in April 2002 from Finnish media group Sanoma in a £36.7m management buy-out, in which ABN Amro Capital invested £9.6m.
Puzzler Media will be one of portfolio of media investments including Parragon Books and the Early Learning Centre.