It’s best to visit Greek islands within the same group. For example, I wouldn’t recommend visiting Corfu and Santorini on the same trip as they’re on opposite sides of the country. Instead, visit islands in the same island group: the Cyclades, the Sporades, the Dodecanese, the Ionian, the Saronic, and the Northeastern Aegean. For one, they’re close to each other. And two, they have frequent ferry connections with each other. For first time visitors to Greece, the Cyclades make the most natural and convenient introduction.
Of the above groups the Dodecanese probably constitute the best opportunity to mix islands between groups. You could, for example, take the Blue Star Ferries and map an island-hopping route that essentially heads in the same direction. In this way you could take in some of the Cyclades – Syros, Mykonos, Patmos, Naxos and some of the Dodecanese – Patmos, Leros, Kos, Chalki, and Rhodes – without any backtracking. Hellenic Seaways is another major ferry company whose routes you may want to explore.
My husband and I are heading to Greece in July this year. We fly into Athens and then are connecting to Samos where we are meeting up for a friend’s 50th birthday celebration. We have 4 nights here and then another week to explore some other islands. We would love to visit Santorini although I know it is not close to Samos so not sure if that is the best option? We thought about Paros or Naxos for 3nts, and then Santorini for another 3nts. Then fly back to Athens and spend a couple of days here before we head for Dubrovnik. Do you know if there are ferries between these Island points and would that be the best use of our time? I guess we don’t want to waste too much time travelling between points! We are just playing around with ideas at the moment as Samos is the only part set in stone. Open to any suggestions as this is my husband’s first trip to Greece and my last trip here was with my parents about 35 years ago! 

Transport between the three islands relies on local ferries and these are unsophisticated ‘landing-craft’ style boats that do little more than ferry passengers and vehicles in Spartan comfort, but they are very functional and vital to the inter-island communication. There is plenty of on the ground support excursions and infrastructure and the islands are well-used to tourism; the only exception is that travellers will need to use a bit of independence in getting between the islands.
Airlines have substantial fixed and operating costs to establish and maintain air services: labor, fuel, airplanes, engines, spares and parts, IT services and networks, airport equipment, airport handling services, booking commissions, advertising, catering, training, aviation insurance and other costs. Thus all but a small percentage of the income from ticket sales is paid out to a wide variety of external providers or internal cost centers.
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