The Philippines, an archipelagic nation of over 7100 islands, has one of the longest coastlines in the world and a highly biodiverse marine ecosystem. The rich marine flora and fauna serve diverse purposes, as food, nutraceuticals, cosmetic products, and traditional medicines. Here, we comprehensively describe natural products discoveries from marine organisms in the Philippines over the past 25 years, covering the chemistry and biological activity. We focus on small-molecule compounds and medium-sized peptides from marine invertebrates, plants, and microorganisms within the Philippine Seas. A total of 403 marine natural products are reported, purified from 56 marine genera, with collections done in 30 provinces across the Philippines. Cytotoxicity and potential anticancer activity is a major theme for small molecules from invertebrates and microorganisms. Peptides from marine mollusks and small molecule compounds from mollusk-associated microorganisms have primarily been assessed for neuroactivity and antipain utility. Members of the Phylum Porifera were the most sampled and studied, with more than 200 compounds reported from 23 genera. Among the different marine genera, significant work has been done in the blue sponge Xestospongia sp.,  Conus spp., and Streptomyces spp. from the Philippines, spanning foundational research on organismal biology to in-depth pharmacological studies of bioactive compounds.