<p>Reefs play an essential role in sustaining life on Earth. They provide food and shelter for many marine organisms, coastal protection from storms and typhoons, and a source of food and income for many coastal communities. Despite their importance, coral reefs are declining rapidly due to natural disturbances and destructive human practices. Over the years, reef systems in the Philippines have been in danger. Thus, this study investigates the extent of this threat to the reef system by identifying the changes in the reef cover. The study’s sites include Tubbataha Reefs and Bolinao, Pangasinan. The study also accounts for the spatiotemporal changes in the reef covers of protected and non-protected marine areas. The data used are Landsat data images (Landsat 5 TM and Landsat 7 ETM+) for a 4-year time interval from 1997 to 2010. Principal component analysis was used to classify the bands representing the reef covers. Both in situ and secondary datasets were used for the validation. Results show a decrease in the coral cover in Bolinao, Pangasinan, over time, while fluctuating patterns for the size of the coral covers of Tubbataha reefs. This implies that both natural and anthropogenic events potentially drive the decrease in coral cover on the reefs. Natural recovery of coral reefs in Tubbataha is also posited, which can be attributed to its classification as a marine protected area and as well as free from nearby coastal communities. The results of this study can serve as a guide for policymakers in crafting tailored interventions to promote coral reef protection.</p>