The reliquary under the Altar enshrines a bronze box by Mamerto Pingol containing earth, corals. and sand from the place of martyrdom of San Pedro in Tomhon, Guam. This is to continue the practice of the companion missionaries of San Pedro and Blessed Diego who used to venerate the ground that was bathed with the blood of the two martyrs.

There is no relic of San Pedro since his body was thrown into the ocean. The bronze box, however, has a portion of the cassock of Blessed Diego and some bones of the martyrs Saint John Nepomucene and Saint Felicity. Two lamps representing the two Archdioceses keep vigil on each side of the bronze box.