Phaistos was first determined in the middle of the 19th century by the British admiral Spratt, while the archaeological investigation of the palace started in 1884 by the Italians F. Halbherr and A. Taramelli. After the declaration of the independent Cretan State in 1898, excavations were carried out by F. Halbherr and L. Pernier in 1900-1904 and later, in 1950-1971, by Doro Levi, under the auspices of the Italian Archaeological School at Athens.

Although many inscriptions were found by the archaeologists, they are all in Linear A code which is still undecipherd, and all we know about the site, even its name are based to the ancient writers and findings from Knossos.

According to mythology, Phaistos was the seat of king Radamanthis, brother of king Minos. It was also the city that gave birth to the great wise man and soothsayer Epimenidis, one of the seven wise men of the ancient world.
Excavations by archaeologists have unearthed ruins of the Neolithic times (3.000 B.C.).
During the Minoan times, Phaistos was a very important city-state. Its dominion, at its peak, stretched from Lithinon to Psychion and included the Paximadia islands. The city participated to the Trojan war and later became one of the most important cities-states of the Dorian period.
Phaistos continued to flourish during Archaic, Classical and Hellenistic times. It was destroyed by the Gortynians during the 3rd century B.C. In spite of that, Phaistos continued to exist during the Roman period. Phaistos had two ports, Matala and Kommos.

Gortys (Gortyna) was an extremely important city during the early christrian period till the Arab conquest. According to tradition, Gortyna was the first city of Crete to accept Christianity. It was the see of the Apostle Titus, first bishop of Crete, whose name bears the basilica. There are many important early Christian monuments inside the archaeological site of Gortyna , which covers a rather large area.

In 1884 the Italian archaeologists Halbherr and Fabricius started the excavations in this site. The Italian Archaeological School continues up to this day the excavatory research under the supervision of the Greek Archaeological Service. During these years, the excavatory research has brought to light a monumental early christian basilica near the archaeological site. The excavations of the 13th Ephorate of Byzantine Antiquities uncover an early christian tetraconch Baptistery.