It connects with the Celebes Sea and to the north and the Banda Sea to the south.
Although the Molucca Basin is open to the Pacific Ocean, deep Molucca Sea water is blocked from entering the Banda or Ceram Seas due to the presence of the Lifamatola sill.
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The Molucca Basin is an area of extreme seismicity, producing numerous high intensity earthquakes and tsunamis in recent time.
Seabed core data from the northern Molucca Sea has yielded rich insights on the paleoclimate of the region, particularly as to details of the last glacial maximum. At that time, approximately 18,000 years Before Present, salinity of the Molucca Basin was deduced to be slightly higher in a decidedly more arid lower atmosphere. Correspondingly, the sea surface temperature was shown to be no more than one degree Celsius cooler than present time.
- E.J.Brill. 1933. The Snellius expedition in the eastern part of the Netherlands East-Indies, 1929-1930: under the leadership of P. M. Van Riel, Volume 2, Part 8
- International Hydrographic Organization. 1953. Limits of Oceans and Seas, 3rd edition.
Tomas Tomascik. 1997. The ecology of the Indonesian seas, Volume 1. Tuttle Publishing. 1388 pages