A team of marine conservationist declared in 2006 that the Philippines is the Center of Marine Biodiversity in the world and Verde Island Passages as the "Center of the Center of Marine Shorefish Biodiversity".
Many threatened species which include sea turtles like hawksbills, olive ridleys, and green turtles; humphead wrasses, giant groupers and giant clams are present in the Verde Island Passage. However, there are no enforcement of ordinances and over-fishing is common. A short-lived 'park fee' scheme for the Verde Island drop-off dive site was soon dropped when it was discovered that the revenue was being used to buy better fishing gear and hence removing fish at a higher rate. Humphead wrasses are especially threatened and divers often go years without spotting a single individual. It was particularly noted the rare red fin wrasse (Cirrhilabrus rubripinnis) thrives in Verde Island.
The area has more than 300 species of corals, which is considered one of the largest concentrations of corals in the country or even in the whole world. Coral health is generally good, though the effects of global warming and increased pollution, may still lead to drop in diversity. The Verde Island passage is located next to Batangas Bay which is rapidly becoming a major refining and petrol chemical center in the Philippines. Until now, no infrastructure is in place to contain a major oil, or chemical spill.