Just came back from Krabi and Phuket 2 weeks back. If you are comfortable staying at hostels then you should check out "Balcony Party Hostel". It's clean and is at the heart of Krabi which is Ao Nang beach. You will never regret spending your money by staying at Ao Nang as it is the best place you can be in Krabi.
In Phuket we stayed at "Paradise Beach Backpackers Hostel" which is at Paradise beach and Just 10 min away from Patong beach. It's a hostel with private beach. I mean it's actually owned by the hostel and the entry is free for the people who are staying in the hostel. Otherwise the entry fee is 200Bhat. Though this place is at a bit segregated area but if you have a bike rented then you wouldn't have any problem. I would prefer this place is you are going to Phuket just for resting. If you need more information then you find my blog on the same in my profile. Or you can also contact me at +918800664705.
It will be rainy in September in the Entire thailand but you will get pretty cheap deals at that time. Mostly rain comes in the early morning and afternoon so if you choose carefully you can still cover most of the places. We stayed in 'Little Home by Ao Nang ' at Ao Nang beach which was pretty awesome. We paid 2500 Rs for their premium room which included a huge room and equally huge balcony.
Try Ao Nang Cliff view resort in Krabi, its just next to a cliff, has a shuttle to beach every hour, has a pool, gym, restaurant. Most of all its densely gardened like cottage in a forest. Most natural habitat for a resort, we also saw peacocks there! I will post some pic on my blog soon.
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