The diversity and distribution of marine macrophytes – including seaweeds and seagrasses – in the Verde Island Passage (VIP), Philippines, was assessed covering nine sites across four provinces (Batangas, Marinduque, Occidental Mindoro, and Oriental Mindoro). Presence-absence data were compared to those of other sites within the VIP collected in earlier studies. Data from the VIP were then compared to sites with similar environmental and geographical features in other parts of the Philippines. A total of 116 macroalgal species and nine seagrass species were recorded from the VIP. This macroalgal richness represents approximately 12% of the reported macroalgae, and the number of seagrass species represents almost half of the known species in the country, suggesting that VIP supports a high diversity of marine macrophytes. Data analyses showed significant clustering of sites within the VIP. Some of the neighboring sites with similar environmental conditions also clustered together. The separation of clusters with sites outside the VIP may, in part, be explained by differences in local environmental conditions such as types of substratum, water depth, and current patterns (water motion). The diversity and uniqueness of marine macrophytes in the VIP highlight the importance of the ecosystem services and functions that these organisms provide. The role of various abiotic and biotic factors in driving variations in macroalgal diversity in the passage needs to be further verified with increased sampling efforts to obtain a more comprehensive understanding of the conservation value of the VIP.