Soderbergh will spend nine weeks filming across Spain, Telecinco Cinema said.
The production company did not release the title of the film, but del Toro's official Web site said it would be called "Guerrilla." The Spain-United States co-production will be filmed entirely in Spanish.
Del Toro's site showed photos of the Puerto Rican actor dressed as Guevara, who helped Fidel Castro overthrow the Cuban government in 1959.
It is the second biography about the famous Argentine guerrilla in recent years following 2004's "The Motorcycle Diaries."
The film reunites del Toro with Soderbergh for the first time since "Traffic," for which del Toro won an Academy Award for best supporting actor for his portrayal of a Mexican police officer.