Geopolitical issues pose a challenge to the holistic management of fisheries and associated ecosystems in two Philippine fisheries management areas (FMAs 5&6) encompassing the West Philippine Sea. One way to allay these issues is through a common values approach based on heritage. This paper presents evidence of the heritage value of FMAs 5&6 that could be integrated into an ecosystem approach to fisheries management to manage conflicts. This presupposes a common understanding of their heritage value and the fundamental principle that sustaining this value is good—in fact, essential—for everyone and our planet. Heritage value is assessed as a composite and dynamic unity of human gains and investments in the ecological value, economic value, and value to society of ecosystem services, which create cultural significance and socioeconomic worth for communities and peoples. Ecological value is assessed by way of selected indications of the ecosystem services of the two FMAs; economic value is assessed using published estimates of the monetizable and nonmonetizable value of these services; and value to society is evaluated based on influences on cultural identities, ways of life, and amenities in surrounding lands and contiguous waters. The values are highly significant and beneficial not only to Filipinos but also to others around the South China Sea and beyond. However, the ecosystem services underlying these values—and users’ access to them—are at risk. They need to be protected from climatic and anthropogenic threats, including illegal, unreported, and unregulated fishing, pollution, coastline modifications, island building, and violations of the United Nations Convention on the Law of the Sea provisions on safeguarding the marine environment and fishers’ safety.