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Haputo, which covers 252 acres of coral reef and limestone forest, was designated an ecological reserve in 1984. Haputo is also listed in the Guam and National Registers of Historic Places.

Historic accounts from the early Spanish era mention that the village of Haputo (sometimes spelled Apoto) was burned in 1678 by Spanish soldiers. In 1680 the surviving residents of Haputo and all the other northern villages of Guam were forced to relocate to Hagåtña.

Although the village was abandoned, it still was recognized by name and located on early European maps of Guam.