A large Roman urban house is currently being excavated west of the ancient theatre. It was built in the 1st century AD, probably after the devastating earthquake of 66 AD. It continued to be occupied as a house, with various modifications, some of which are visible in places in its masonry, until it was destroyed in the great earthquake of 365 AD. In the following centuries (5th- 7th c. AD), the area was only partially reused.

Laid out around the courtyard with its peristyle of Greek origin, the house extends south to north across a large area (the current excavated area measures 765 m 2 ). The entrance was via a vestibule opening off the paved public street to the south of the house; running east-west, this is probably the continuation of the street beginning at the west parodos of the theatre. A double doorway led to the vestibule with the household shrine (lararium). In the destruction layer of 365 AD was found an important statue group of Artemis and Apollo, the tutelary deities of the city, in bronze and marble respectively, set on a single stone base.

The atrium does not have the typical features of the Roman atrium. Instead of an impluvium (a cistern in the floor of the courtyard for collecting rainwater from an opening in the roof), it has a large cistern in a space to the south, its opening incorporated in the west wall. Next to the cistern is a stone fountain base, while on the bottom of the cistern was found an intact clay water jar of the late 3rd – early 4th century AD. Nearby was a stone olive press bed (trapetum), probably moved here from its original location, and a stone mortar, indicating that, at least during its final phase of use, this part of the house was used for everyday activities.

The atrium, which would have provided the house with light and air, is surrounded by a peristyle of Greek origin with a stylobate and 5 x 7 columns with Ionic bases and Doric capitals. Most of the column drums and some of the capitals are visible, fallen inside the courtyard in a way indicative of destruction by earthquake. Peristyle courtyards generally contained gardens (viridaria), and this is also true of the Aptera house, as the excavation has uncovered small decorative sculptures and a marble table base. The tile-roofed stoa surrounding the peristyle would have been decorated with colourful wall paintings.

West of the atrium are the bedrooms (cubicula), according to the typical layout of urban houses, while the room west of the cistern, opening onto the peristyle, may have been a dining or reception room.

Even more elaborate variations on the urban house (domus) of Aptera are found in other Cretan cities, such as Kissamos, Eleutherna and Knossos, and also in Pompeii. With the addition of the peristyle courtyard, these houses follow the basic architectural type of the Hellenistic period.