Raja Ampat lies on the equator with 12 hours of daylight from 6.00 am to 6.00 pm all year round. The temperature is quiet constant: the average temperature is minimum 25°C at night time and up to 31°C during the day. It often feels hotter due to the high average humidity of 87%. The ocean temperature is constantly pleasant 29 °C.  The months between May and September, December and January are statistically the wettest. But it doesn`t mean it`s raining all the time, like in Bali or Malaysia. There is no particular rain season, occasional heavy rain shower are quite normal all year round. It usually rains only a couple of hours at a time. Just jump in the warm ocean and wait the shower to finish. Rainy days also spread an magical atmosphere. Sometimes you sit on Gam island in the sunshine, while watching heavy rain pouring down on the next island. At night you are often able to watch beautiful stars and lightening from a storm far away at the same time.
Windy season starts from June till September. Occasionally winds can occur from the south, which makes the ocean little choppy and less pleasant. Most of the homestays are open all year round, except some homestays in Misool in the south, due to the long distance and the uncertain weather conditions. The central of Raja Ampat included Gam Island, can be visited all year round. Only the small boat traffic between the islands might be limited, based on  weather conditions. The visibility of the water is not affected by the southerly winds. On the contrary. The visibility is better with crystal clear water during the windy season. You might find that from October till April the visibility can be affected by plankton. However this means it's Manta season. Most people visit Raja Ampat from October till May. There are less tourist during the windy season. Perfect conditions for underwater photography. Crystal clear water, visibility more than 30 meters and most of the time you`re the only boat on the dive site.
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Conclusion:
Winter season: Manta season, less wind but reduced visibility.  Summer season: Awesome visibility, less crowded dive sites, but low chance of Mantas and rougher ocean.
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You can visit Raja Ampat all year round; any time has it`s advantage and is simply beautiful.