In the historical times, although some of the residents were Dorians and they were under the influence of Sparta, Anafi joined the Delian League, paying annually 1000 drachmas. After the Capture of Constantinople in 1204 by the Franks, it came to Marco Sanudo, who ceded it in 1207 to the Venetian Leonardo Foscolo. At that time the island was known by the corrupted name Namfio.
In 1269 the formidable pirate of Anafi, John Delokavos, liberated it from the Latins, but in 1307 it came under the dominance of Giannoulis Gozzadini from Bologna. From 1397 Anafi was attributed to the house of Crispo. With the treaty of 1419 between the Ottomans and the Venetians, along with other Cycladic islands it remained under the rule of the Venetians. Then Jacopo Crispo gave it to his brother William, who after the death of his nephew and heir of the ducal throne John Jacopo Crispo in 1453 was proclaimed Duke of Naxos ceded Anafi to his daughter Fiorentza. In 1528 due to hereditary right the turn of the house Pisani to rule the island came, but in 1537 it was occupied by Barbarossa to become tributary to the Venetian Bailo (Consul) in Istanbul. As regards to the ecclesiastical state, Anafi from 1571 belonged as an Exarchate to the Archbishop of Santorini, while in 1646 itbecame of the archdiocese of Sifnos.
The island continuously suffered from pirate raids, especially in the 15th century by Turks and Catalans, so many residents sought refuge in Crete. The building Crispo of the castle Gibitroli on the east of the island close to the church of the Virgin Mary Kalamiotissa by William II is related to pirate raids. Painful memory is the looting in 1799 by pirates. During the reign of King Othon residents of Anafi went to Athens to offer their work in the rebuilding of the new capital. They created the picturesque neighbourhood of Anafiotika down the north side of the Acropolis.