It is located in the Luzon Strait north of Luzon Island and south of Taiwan The town is composed of four of the five major islands of the Babuyan Islands namely: Calayan, Camiguin, Dalupiri and Babuyan Island. Calayan Island is the largest of the Babuyan Islands. Fuga Island, the fifth island within the Babuyan Islands, is part of Aparri municipality. Calayan is home to the Calayan rail, a flightless bird identified as a separate species in 2004 and endemic to Calayan Island.

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