It is known from archaeological finds in the area that there have been settlements here dating back to the 9th Century BC. The Minoan artefacts and the ruins found in Makriyialos certainly provide evidence of population around the time when the Minoans were the most advanced civilisation in the western world (approximately 1800 to 1630 BC).

There are also the remains of a Roman Villa on the headland above the port of Makriyialos. In 74 B.C. the consul Mark Anthony began a campaign against the island, but the Cretans were well-prepared and defeated him at sea. Yet, in 69 B.C., Crete fell to the Romans and was a Roman province until 369 A.D and it was during this period that the villa was built.

The first Byzantine era (395 A.D. until 824 A.D), the Arab invasion (824 A.D until 961 A.D) and the second Byzantine era (until 1204 A.D) have left no lasting imprint on the region, although the subsequent Venetian rule has left some influences in the region, namely at Etia, near Handras. It was at this time villages in the area were first recorded. One example is Ayios Stephanos, which was recorded in the Venetian census during their occupation of Crete in 1577. The return of Turkish rule in the period 1646 to 1669 brought traumatic times to the area. Many inhabitants fled Crete to escape the persecution of the Ottoman government, while thousands of others became prisoners or fled to the mountains.

Whilst various occupying nations held power in the island from the Venetians to the Turks, the thriving village communities in the hills around the area show that there had been a small but itinerant population living mainly on the hillsides. Finally, in 1913, union with Greece was realised with the leader of the Cretan rebellion against Turkish rule, Eleftherios Venizelos as Prime Minister.

Crete was occupied during the Second World War and was the scene for many well documented and heroic acts of resistance by the local population although it was one of the last Allied areas to be released from occupation after the fall of Berlin. At the end of World War II, Crete began reconstruction while the rest of the country was embroiled in a civil war. Due to this period of peace and also due to its favourable climate, the island became one of the most prosperous areas of Greece with agricultural products becoming a mainstay of Cretan economy.

Today, tourism provides another economic boost to the island. Infrastructure built in the last twenty years accommodates this latest influx of foreign visitors. The superb climate and diverse beauty of the island beckons visitors from all over Europe. In 1926 the first Greek census of Crete listed the population of Makriyialos as consisting of 12 residents, but it is, however, within the last thirty years that the populations of these mountain villages have migrated in large numbers to the coastal settlements, due almost entirely to the tourist trade.