It is located on the site where the island's first Catholic church was constructed in 1669, under the guidance of Father Diego San Vitores.

The precursor of the present day basilica was a chapel, or capilla, constructed of rough logs and nipa thatch built within the perimeter of the Plaza de España.

Built under the direction of Padre Diego Luís de San Vitores, with the assistance of the Chamorros of Hagåtña, it was dedicated on February 2, 1669.

According to historian Benigno Palomo, in 1669, one of the main missions of the Spanish soldiers and missionaries was to exalt "the Catholic faith" and that "the people living in islands and land of this sort, you will and ought to bring to the Christian religion", from the Bill of Partition issued by Pope Alexander VI.

The cathedral-basilica serves as local landmark and is home to a community of parishioners who regularly attend Sunday Masses, sacred liturgies and annual events.