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The area known as Croatia today has been inhabited throughout the prehistoric period, ever since the Stone Age.

In the middle Paleolithic period, Neandertals lived in modern Zagorje, northern Croatia. Dragutin Gorjanović-Kramberger discovered bones and other remnants of a Neandertal, subsequently named Homo krapiniensis, on a hill near the town of Krapina.

In the early Neolithic period, the Starčevo, Vinča and Sopot cultures were scattered between and around the Sava, the Drava and the Danube. Notable are the excavation sites of Ščitarjevo near Zagreb, Sopot near Vinkovci, Vučedol near Vukovar, Nakovanj on Pelješac. Traces of a somewhat isolated Hvar culture were found on the Adriatic island of Hvar.

The Iron Age left traces of the Hallstatt culture (proto-Illyrians) and the La Tène culture (proto-Celts).

In recorded history, the area was inhabited by Illyrian tribes such as the Delmetae, who spoke an Illyrian language, an ancient branch of Indo-European. Other tribes such as the Liburni and Iapodes, whose ethnicity is less clear, inhabited various parts of the Adriatic coastline and interior between modern Istria and Herzegovina.

In the 4th century BC the northern parts of modern-day Croatia were also colonized by the Celts, the Scordisci tribe. Other Celtic peoples may also have been found elsewhere integrated among the Illyrians. The islands of Issa and Pharos as well as the locality of Tragurion became Greek colonies since the same period.

Illyria was a sovereign state until the Romans conquered it two centuries later, in 168 BC. The Romans organized the land into the Roman province of Illyricum which encompassed most of modern Croatia (Istria was part of the province of Italia). Illyricum was subsequently split into the provinces of Pannonia and Dalmatia in year 10. Pannonia was further split in two by Trajan between 102 and 107.

A four-fold split of the same province followed at the turn of the 4th century under Diocletian — an emperor of Illyrian descent, from Dalmatia. Other notable people from these areas in this period included the Christian Jerome, Saint Marinus (builder of San Marino), emperors Valentinian I and Valens, and Pope John IV.

After the fall of the Western Roman Empire in the 5th century, the Roman roads and the Illyrian population speaking Romance languages (such as Istro-Romanian or Dalmatian) remained. With the increasing amount of human migration, this population entrenched in the cities along the whole Dalmatian coast.

The Lombards and the Huns made an incursion from the north. After 476 the area was subject to Odoacer and then to Ostrogoth rulers beginning with Theodoric the Great. Justinian claimed the old province of Dalmatia to the Eastern Roman Empire in 535. Forebears of Croatia's current Slav population settled there in the 7th century following the Avars, reportedly under instructions from Byzantine emperor Heraclius.