The archaeological site of Eleutherna, Crete, covers a vast area, which includes the Nisi and Pyrgi hills in the modern villages of Eleutherna and Ancient Eleutherna respectively. Hellenistic retaining walls, the remains of a Roman settlement, and an Early Christian basilica were excavated at Katsivelos, at the east foot of Pyrgi hill, and a Late Geometric/Archaic cemetery, which is partly covered by a Roman building, was revealed at Orthi Petra, on Pyrgi's west slopes. The remains of a Hellenistic settlement were identified on Nisi.

According to a dedicatory inscription, the Early Christian basilica at Katsivelos was built in 430-450 AD and dedicated to the Archangel Michael. The basilica was founded on the ruins of a Hellenistic sanctuary, which remained in use in the Imperial period, and was destroyed in the seventh century AD. Forty-two tile and cist graves of the sixth and seventh centuries were identified inside and around the temple and the basilica. West of the basilica are the remains of three Roman houses, which were destroyed by an earthquake in 370 BC, a Roman bathhouse with two hypocausts, a paved road, and a large, possibly public building of the Hellenistic (second-first centuries BC) and Roman (first century BC-second century AD) periods.

Architectural remains primarily of the Roman and Late Roman periods were also revealed on the northern plateau of Pyrgi hill, where the ancient city's nucleus is believed to have been always located. At Orthi Petra, on the west slope of Pyrgi hill, is the late Early Geometric - early Archaic (870/850-600 BC) cemetery, which features different burial practices (open burials, cremations) and various architectural constructions (enclosures, grave courts, monuments).

Research at Nisi hill revealed a settlement of the Hellenistic period, which was abandoned at the beginning of the Roman period. A characteristic feature of the settlement is that each residence had its own water cistern to ensure its water supply. A rectangular enclosure with a pentastyle Doric propylon of the Classical period (400 BC) was also discovered in this area.

Other archaeological remains and isolated monuments have been identified in the area, but not excavated. Among these, the tower at the top of Pyrgi hill, which was used from the Hellenistic until the Byzantine period, and the Hellenistic bridge north of Pyrgi hill are particularly noteworthy.