[4] Waitanta was first inhabited by humans over 50,000 years ago and excavations at Mololo Cave indicate people were making tree resin artefacts and hunting native animals.

[7] Islam first arrived in the Raja Ampat archipelago in the 15th century due to political and economic contacts with the Bacan Sultanate.

[9] Alfred Russel Wallace spent some time on the island and studied the flora and fauna during the late 1850s while on his scientific exploration trip.

Since 1997, the island has been the site of a substantial pearl farming operation owned by the Australian company Atlas Pacific.

[citation needed] Languages spoken on Waigeo include Papuan Malay, Biak, Ma'ya, and Ambel.