The most important monuments of the site are:
Church of Agios Stefanos ? Early Christian Basilica
The church, which survives today and is dedicated to Agios Stefanos (Saint Stephan), is built on the ruins of an Early Christian basilica, probably dated to the mid 6th c. A.D. The basilica was three-aisled, with a double narthex and an apse at its middle aisle. Along its northern side, there was an oblong adjacent structure with a small apse. After its destruction, probably due to an earthquake, the church of Agios Stefanos with two vaulted aisles was built on its ruined middle aisle. Constructed with ancient architectural members, mainly from the basilica, the church is dated to the 8th or 9th c. A.D., when the inhabitants of Thera, as well as of the other islands, suffered from the invasions of Arabs and their constructions were rough and modest, contrary to those belonging to the Early Christian centuries. The two Christian monuments are eloquent witnesses of the inhabitation of the city even after the ancient times.
Temenos of Artemidoros
The temenos was founded in the mid 3rd c. B.C. Its founder and priest Artemidoros of Apollonios from Perge of Pamphylia, driven by a dream that he saw, settled in his old age in Thera. For the activity he developed, founding sanctuaries and embellishing the city, he was honoured twice with an olive wreath and was granted the right of the citizen of Thera. The open-air sanctuary was chiseled out of the rock by Artemidoros himself: altars, relief decorations and numerous inscriptions, mainly epigrams for the honoured gods and for Artemidoros, cover the front side of the rock, whereas statues decorated the place; this is also where the resolutions of the demos of Thera in honour of Artemidoros were placed. From the right to the left, three steps with inscriptions in honour of Hecate and Priapos are carved, as well as the altars of the Dioskouroi, Omonoia and the gods of Samothrace, the eagle of Zeus Olympios, the lion of Apollo Stephanephoros -the throne of the goddess Tyche in the front- and the dolphin of Poseidon Pelagios. The set is completed by the portrait of Artemidoros depicted wearing a wreath; in the surrounding inscription he expresses his wish that his name remains immortal in eternity.
The imposing oblong structure with the Doric colonnade on the long axis that dominates the south ágora served official and civic purposes and was undoubtedly the administrative centre of the city. Its erection dates to the early 3rd c. B.C., however, in the course of time, the building underwent repairs. Two slabs of stone, which were built-in opposite the entrance, refer to an extended repair that took place in the mid 2nd c. A.D. On one of them is inscribed the public promise (eisaggelia) of the citizen T. Flavius Kleitosthenes Claudianus that he would take upon him the cost of repairing the building and on the other a resolution adopted by the assembly of the citizens (ekklesia of demos) and the council (boule) in his honour for his benefactions offered to the city. During this repair, the north part of the building was transformed into a special area with a pedestal for the erection of statues, which appears to have been dedicated to the worship of the Roman Emperor and his relatives. Moreover, the building was embellished with a rich sculpted decoration. According to the inscriptions, the "Basilike Stoa" or "the Stoa at the agora", as it is called, was an old and distinguishable building, an ornament to the city.
Built near the agora, in the densely structured centre of the city, the theatre was also used, according to epigraphic testimonies, as a bouleuterion. Despite its small size and its simple architectural form, it belonged to the most imposing buildings of the Hellenistic ? Roman city. At its place probably pre-existed a simpler construction used for assemblies. The theatre appears to have been constructed in parts in the 2nd c. B.C. On its north side, the only one with no adjoining buildings, there were two entrances, the one on the higher part towards the auditorium and the other towards the orchestra. Six stairways in radial order divided the auditorium, which had a capacity of about 1.500 persons, in five wedge-shaped seating sections. The scene building, with a stone proscenium, left the circular space of the orchestra free. In the 1st c. A.D was constructed a Roman type scene building with proscenium, decorated with statues of the imperial family, which occupied part of the orchestra. Under the auditorium, a big cistern collected rain water. The oblong building in the west of the theatre was built at the same time with the auditorium, but still remains unknown whether it was linked to the theatre from the inside or had some other public use.
Sanctuary of Apollo Karneios
The south end of the crest where the central street ended, away from the noisy centre of the city, constituted, from the time of its foundation, an important cult centre. Apollo Karneios held a prominent position in the area, with a sanctuary and a big artificial terrace for his annual festival, the Karneia.
The cult of Apollo Karneios, God of the Dorians, dominated the religious life of the inhabitants of Thera throughout antiquity. The sanctuary in honour of the God was erected at a conspicuous place in the city, probably in the 7th c. B.C. The area of the sanctuary was defined by an impressive enclosure with an entrance from the sacred way decorated with a small propylon. Today only the traces of the propylon remain on the rocky ground. The areas of the sanctuary are developed in a line. The entrance opens at the central court; two footprints, engraved on the threshold of the entrance, witness until today the passing of a worshipper. On the right side of the courtyard, there is a building of undetermined use, while on the left side, in a higher level, there is the temple with its forecourt. Two magnificent entrance gates led from the court to the forecourt of the temple, which was decorated with a mosaic floor in the 3rd-2nd c. B.C. The temple, a simple oikos with a flat roof, comprised the pronaos, the cella and two side rooms, probably adyta. Among the four columns that supported the roof of the cella must have been placed the god?s acrolithic cult statue.
Gymnasium of the Ephebes
A great number of inscriptions of the 2nd c. B.C. to the 2nd c. A.D. indicate the use of the building, however, the small number of construction remains do not allow an interpretation or accurate chronology of its different areas constructed gradually. The natural cave ?place of cult since the Archaic times? which was transformed into a sanctuary dedicated to Hermes and Hercules, patron divinities of the gymnasium, constituted the core of the facility. The areas of the gymnasium were organized around a big courtyard, where led a stone-paved stepped street. Building remains survive only on the north and east side of the courtyard, as its south part has crumbled to a large extent down the steep slope. Its north side consists of two spacious rectangular rooms that open at the courtyard, while the east side consists of smaller rooms and a circular structure, probably the aleipterion, mentioned on an inscription, that is, a heated structure, where the ephebes bathed and anointed their bodies with oil before and after the exercise. The gymnasiarch was responsible for the running of the gymnasium, assisted by the hypogymnasiarch. According to epigraphic evidence, contests in the nude were carried out, which comprised the events of wrestling and pankration. On the exposed sections of bedrock near the gymnasium multiple inscriptions with names of the ephebes are found.
Sanctuary of Egyptian gods
During the Hellenistic times, a period of great receptivity to new gods and cults, the worship of eastern and Egyptian deities is spread across the Greek territory. In Thera, the Egyptian gods Serapis, Isis and Anubis become accepted in the early 3rd c. B.C. and their cult is quickly integrated into the public and private religious life of the inhabitants of the island. The cult of the Egyptian triad of gods in Thera, which, in this period, belongs to the possessions of the Ptolemies is closely associated with the presence and activity on the island of a large Ptolemaic Garrison. A sanctuary in honour of the Egyptian gods is founded in the first half of the 3rd c. B.C. The sanctuary consisted of an unusual outdoor construction, that is, a terrace, constructed mainly with artificial earth fill, the two sides of which were defined by the rocky land. Today survives mainly the rock-cut part of the sanctuary, with niches for votive offerings on one side and a bench for the placement of cult statues on the other.