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The working title of this film was The Gun and the Cross. In a spoken foreword, the film announces that only "one language" would be used in the dialogue, despite the varying ethnic backgrounds of the characters. In the onscreen credits, actor Julio Villarreal's surname is incorrectly spelled "Villareal."
According to an August 1954 Hollywood Reporter news item, Edward Dmytryk was originally assigned to direct the picture. According to an January 18, 1955 Hollywood Reporter news item, Cameron Mitchell had been cast in a lead role, and in February 1955, Hollywood Reporter announced that singer Russell Evans was considered for a part in the picture. Hollywood Reporter news items include Felipe Mndez, January Svelk, Jaime Rosario, Jack Maner and Gilda Fontaine in the cast, but their appearance in the completed picture has not been confirmed. A April 4, 1955 Hollywood Reporter news item stated that the "famous choir" of Franciscan Cathedral Toluca, a four-hundred-year-old church near Mexico City, was going to be used in the film for "special choral effects," but the choir's participation in the released picture has not been confirmed.
Seven Cities of Gold was mostly filmed in Mexico, in and around the west coast town of Manzanillo and the deserts of Guadalajara. An Indian village was built as a set in the hills near Manzanillo, and a reproduction of the original San Diego mission was constructed on the beach. Although studio publicity material credits Mexican director/producer Ren Cardona as Robert Webb's co-director, and Mexican director of photography Jorge Stahl as Lucien Ballard's camera operator, it is likely that they were hired only to fulfill union requirements and did not actually work on the production. A few sequences of the picture were shot on location in Topanga Canyon, CA, according to a May 19, 1955 Hollywood Reporter news item.
As depicted in the film, in 1769, Padre Junpero Serra (1713-1784) accompanied the expedition of Jos de Galvez to Upper California and founded the Mission San Diego de Alcala. It was the first of twenty-one Franciscan missions established in California. On September 25, 1988, Serra was beatified, the first step leading to sainthood in the Catholic Church. The Motion Picture Herald reviewer remarked that Seven Cities of Gold was the "first important film dealing with" Serra's contributions, while the Hollywood Reporter review commented that it was "the first film to pay attention to the important contributions of culture and humanity made by the Spanish to the development of more than half of the new world." Director-producer Webb and producer Barbara McLean were married at the time of this production. Seven Cities of Gold marked the first producer assignment of longtime Fox film editor McLean.