Having just returned from a 4 day stay in Naxos, as well as Mykonos, I must recommend Adriani studios, This block of studios has recently been renovated to give studios of varying sizes. This main attraction is the view. The studios are at the port side of town, 300mtrs from the port, and there is a superb seaview looking out to the gateway of the temple of Apollo on the Palatia islet. Seeing the sunset from the balcony is to die for.
The studios are superbly clean, if small, but ideal for a short stay. They are owned and run by Micheal Kritikos and his family.
Michael will transport you from ferry port and airport. They also have a small hotel nearby, newly refurbished and very smart
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