The Molucca Sea is located in the western Pacific Ocean, around the vicinity of Indonesia, specifically bordered by the Indonesian Islands of Celebes (Sulawesi) to the west, Halmahera to the east, and the Sula Islands to the south. The Molucca Sea has a total surface area of 77,000 square miles. The Molucca Sea is rich in coral and has many diving sites due to the deepness of its waters. The deepness of the water explains the reasoning behind dividing the sea into three zones, which functions to transport water from the Pacific Ocean to the shallower seas surrounding it. The deepest hollow in the Molucca Sea is the 15,780-foot (4,810-meter) Batjan basin. This region is known for its periodic experiences of earthquakes, which stems from the sea itself being a micro plate, in which the Molucca Sea is being subducted in two opposite directions: one in the direction of the Eurasian Plate to the west and the other in the direction of the Philippine Sea Plate to the east.

The Banda Sea is one of four seas that surround the Maluku Islands of Indonesia, connected to the Pacific Ocean, but surrounded by hundreds of islands, including Timor, as well as the Halmahera and Ceram Seas. It is about 1000 km (600 mi) east to west, and about 500 km (300 mi) north to south.