Indonesia has a diverse range of cetacean species, yet there are few records of their distribution, especially from remote regions. Incidental sightings from aerial surveys were conducted in 2006 and boat-based surveys were conducted from 2006–2011 in Raja Ampat in the Bird's Head Seascape, Indonesia. This paper is the first to provide a species list and an indication of the spatial and temporal distribution of cetaceans in central and southern Raja Ampat. Seven dolphin and six whale species were documented, including Indo-Pacific humpback dolphins Sousa chinensis, Bryde's Balaenoptera edeni, sperm Physeter macrocephalus, killer Orcinus orca and pygmy killer Feresa attenuata whales. Temporal differences in sightings suggest Raja Ampat is an important area for migratory whale species and resident populations of Indo-Pacific humpback Sousa chinensis, spinner Stenella longirostris and common bottlenose Tursiops truncatus dolphins. Cetacean diversity was highest in the months of January–February, May and October–November, with most sightings recorded in Kofiau marine protected area and Dampier and Sagewin Straits. Diversity and species distribution data are critical for managing cetaceans in Indonesia. Emerging threats to cetaceans in Raja Ampat include seismic surveys for seabed oil and gas exploration, potential strikes from increasing ship traffic, entanglement in fishing nets and increasing discharge of plastic pollution from urban areas. In addition to regulations for marine protected areas, a wider conservation strategy is required to address or better manage emerging threats to Raja Ampat, and to ensure the long-term protection of resident and migratory dolphin and whale species.