Portuguese texts resisted the use of Spanish holonyms for naming the Philippines during the sixteenth century and up to the dynastic transition of 1580, when Philip II became king of Portugal. As a result of their maritime ventures, the Portuguese spatial perception of the present-day Philippines differed from that of Spanish officials, by not recognizing a specific identity for the archipelago within the context of South East Asian islands. This article analyses the place of Mindanao in the Portuguese spatial understanding of Island South East Asia by focusing on ethno-historical accounts and chronicles as well as manuscript cartography from the sixteenth century. The combined study of these sources demonstrates that from the 1520s through the 1570s Mindanao occupied a very different place in the Portuguese geographical mindset of the region. This only changed with the formal end of Iberian confrontation in South East Asia and not without Portuguese narratives on Mindanao also being incorporated into Spanish texts. The article focuses on an earlier stage in the construction of the Philippines’ geographical identity, one in which Mindanao occupied a more central role, and its echoes and influence on later Spanish texts destined to convey a unitarian, integrated view of the archipelago.