Ambon island lies in the central part of the Moluccas (Spice Islands) and consists of two peninsulas (Leitimor and Hitoe) connected by a narrow neck of land. The bay thus formed cuts about 20km into the island with the airport on the northern shore and the city of Ambon on the southern side.
The diving in Ambon is mainly done in the Ambon Bay and you come here basically for the great muck-diving. Be prepared for some interesting critters and amazing behavior! The most well known dive site, the Twilight Zone lies close to the airport (northern side of Ambon Bay, close to the Maluku Divers) and is an area, where you can find some very special animals like Rhinopias scorpionfishes, frogfishes, seahorses, stonefishes, ghostpipefishes, pegasus sea moths, mandarin fishes, nudibranchs, harlequin and coleman shrimps, kauris, wonderpus, mimic and flamboyant cuttlefish. This is also the area where the famous psychedelic frogfish (Histiophryne psychedelica) was found.
For coral diving there are also some really nice places you should visit, for example Pulau Tiga, a group of tiny islands in the western tip of Ambon or Pintu Kota or Hukurila Cave in the south side of Ambon island where you can do wall diving and dive in caves and swimthroughs. Several nice dives sites are found around Saparua, specially to the south, around the cape and Molana island and Nusa Laut. Here you find mostly large schools of fish, pelagics like tunas and jacks and sharks. Specialized muck-diving operators like Maluku Divers seldom dive here, you would have to try some of the other dive operators (Paperu Resort, Blue Rose Divers) or liveaboards.
The best months for diving are September to December and March to April but also the months between. The Moluccan islands have the seasons reversed from the rest of Indonesia, when they have the dry season, its rainy season in Indonesia and vice versa. Visibility is usually good (20-30m) except some muck sites close to the harbour or where sand is easily stirred up.