1. Sipadan Island, Mabul Island and Kapalai Island
These three islands probably contain the best dive sites in the whole of Malaysia. Sipadan is by far the best place to enjoy scuba diving; it is also not that easy to actually dive at because of the restricting rules that are in place (daily permit). Mabul is known worldwide for its amazing muck diving conditions. Kapalai is a small sand bank, not that great for diving, but here you can find a very exclusive resort built on stilts. Actually both Sipadan and Mabul earn their own spot in this list, but since you can’t visit one (Sipadan) without the other (Mabul) we just listed the whole cluster as one entry. – wonderfulmalaysia.com
2. Lankayan Island
Lankayan Island is a small island located in eastern Sabah and this island is all about diving and relaxing. However, if you are a non-diver, it’s best you visit other islands as accommodations in Lankayan Island is cheaper for divers.
3. Layang-Layang Island
Layang-Layang is located in a remote area, where the underwater world has not been affected by human beings. Corals are in pristine conditions. Layang-Layang is a place to see big species and big schools of fish.
4. Mataking Island, Pom Island and Sibuan Island
The area surrounding Mataking, Pom and Sibuan offers quite a few amazing dive sites (especially Sibuan which is known for great muck diving).
5. Redang Island
Redang island is located within the Terengganu Marine Park, nearby the city of Kuala Terengganu. It offers great dive sites and it is also a great place to start with your diving adventure as prices of their diving course are very affordable.
6. Lang Tengah Island
Located between the more popular islands of Redang and Perhentian, the smaller island of Lang Tengah offers great diving opportunities. The island has a few nice resorts, and is also suitable for non-divers. Lang Tenggah cannot be visited between October and March because of the monsoon season.
7. Tenggol Island
Tenggol Island is an island off the coast of Terengganu that offers splendid diving conditions. However, it is not suitable for beginners due to the currents that often play a big role in dives around the island.
8. Tioman Island (and the surround islands)
Tioman Island is a small island in Pahang which is a great location for diving, snorkeling, sunbathing and kayaking. The only downside with Tioman Island might be that is not that easy to reach compared to other islands, unless you are willing to pay a little extra for the direct KL -> Tioman flight operated by Berjaya Air.
9. Perhentian Island
The Perhentian Islands are a small group of beautiful, coral-fringed islands off the coast of northeastern Malaysia in the state of Terengganu. It is the best island in Malaysia to do a diving course and snorkeling as well. At Perhentian prices for fun dives and for the diving course are probably the lowest in Malaysia. If you are a beginner, Perhentian Island is definitely the place to be!
10. Tunku Abdul Rahman Marine Park
Similar to Perhentian, Tunku Abdul Rahman Marine Park is also a great places for beginners. It is located right opposite of the city of Kota Kinabalu in western Sabah and this area contains numerous dive sites that are definitely worth a visit.