Looking for advice on places to dive within the Philippines

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So you are not interested in macro/muck and wreck.
Fly into Tacloban, private/public transfer to Sogod Bay(diving), ferry from Bato to Ubay(Bohol), public or private to Alona Beach(diving), ferry to Dumaguete, transfer to Apo Island, back to Dumaguete, ferry and bus to Cebu City, public/private transfer to Malapascua(thresher shark) and finally return to Cebu City to fly home via Manila.
There are a lot of travelling in this suggestion. But you can easily leave out couple of places or add Moalboal on the return journey from Dumaguete to Cebu.
I've been looking into this itinerary more along with my preferences. I think I'm going to skip out on Malapascua -- it's a bit far out of the way and I'm not sure if I like the idea of seeing sharks that much to go.

It looks like my trip is going to be focused around Bohol, Apo Island, and Moalboal. I'll have to do more research on Southern Leyte / Sogod Bay since I haven't looked into it.
 
Planning to be in the PH from mid-March to mid-April
Weather should be fine generally.
I've been looking into this itinerary more along with my preferences. I think I'm going to skip out on Malapascua -- it's a bit far out of the way and I'm not sure if I like the idea of seeing sharks that much to go.

It looks like my trip is going to be focused around Bohol, Apo Island, and Moalboal. I'll have to do more research on Southern Leyte / Sogod Bay since I haven't looked into it.
Malapascau + Southern Leyte would be my first choice if I never been diving in Visayas.
Still possible to see whaleshark in Southern Leyte in Mar/Apr. There is no guarantee on this.
They are free swimming and not being fed.

If you do not mind a bit of travelling than add Bohol.
Some divers like Apo Island because of its rustic style on lodging. Diving is very similar as Balicasag.
 
I think I'm going to skip out on Malapascua

Interesting comment. It’s only 3 hour drive from Cebu city and half hour boat ride to Malapascua.

I think this Thresher shark cleaning station in Malapascua is the only place in the world that I know of to be in close encounter with Thresher Shark. That’s my main reason to go half way around the world to Philippines, to see them.

I have seen Thresher shark in a distance when I was diving in Indonesia. They are very skittish. They swim off as soon as they see divers. In Malapascua, they are still skittish but if you just hover quietly a meter off the bottom, hold breath while videoing them without video or strobe lights, they won’t see you and would come closer to you.

And @matt_reed recently posted this:
Malapascua - not just Thresher sharks
 
which liveaboards would you recommend?
One that you can get space on, for one thing. They do tend to book up so best to plan ahead.

We were happy with Atlantis Azores. There are many boats that do it, or at least used to be. Might check live aboard.com to get general idea what's available.
 
which liveaboards would you recommend?
There is absolutely no need for recommendation if you are looking for a berth for this coming season.
The season is very short but I would not recommend the beginning or the end of it.
Best time is Apr to late May. June is too late.
One that you can get space on, for one thing. They do tend to book up so best to plan ahead.

We were happy with Atlantis Azores. There are many boats that do it, or at least used to be. Might check live aboard.com to get general idea what's available.
Well said.
Option is very limited by now.
 
https://www.shearwater.com/products/peregrine/

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