The Chocolate Hills in Bohol is one geologic phenomena most people know little of. Here’s one of the more accepted scientific explanation about it as printed in a bronze plaque at the top of the Chocolate Hills Complex View Deck.
About 2 million years ago, most of the island of Bohol was below a shallow sea coral reefs, similar to those now found offshore of Northern Bohol, thrived and extensibly covered the sea floor. During stormy days, fragments of coral and shells derived by waves from the reefs were deposited were mostly deposited in the landward side of the reefs. The coral and shell fragments formed relatively thin layers surrounding the live coral reefs.

Slowly, the land rose causing the coral reef formation to emerge out of the sea. The taller arrows shown in the diagram indicate that the southern sections of Bohol island have been uplifted more than the northern section.
The Chocolate Hills have been carved out from the relatively thin layers of coral and shell fragments. Gullies were developed in the low lying areas and lakes occupied pre-existing depressions.
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