In 1999, GONZO merged with Digimation to form Gonzo Digimation Holdings, one of Japan's premier digital animation production companies. The new merged company's name was Gonzo Digimation. This name was changed back to Gonzo in July 2004.

Shouji Murahama first imagined the company as a group of ruffians; therefore, he chose the name "GONZO" as it means "ruffian" in the Italian language.