These main islands are, counterclockwise starting from northeast, Babuyan, Calayan, Dalupiri, Fuga, and Camiguin.

[1] The largest of these is Calayan with an area of 196 km2 (76 sq mi), while the highest peak in the island group is Mount Pangasun (1,108 metres, 3,635 ft) on Babuyan Claro.

The Babuyan archipelago, along with the nearby Batanes islands, have been designated an Important Bird Area (IBA) by BirdLife International because they support significant populations of resident Taiwan green pigeons, Ryukyu scops-owls and short-crested monarchs, Chinese egrets on passage, and wintering yellow buntings.

[9] The island group is also a congregation site for endangered humpback whales, one of few in Southeast Asia.

[14] Babuyan and Dalupiri are themselves individual barangays in Calayan municipality, respectively named Babuyan Claro and Dalupiri, while Fuga Island is also an individual barangay, also named Fuga Island, in Aparri.