Archaeological excavations that were carried in Makronisos area, a rocky area to the west of Ayia Napa, unearthed nineteen carved tombs. It is believed that in the ancient times, the area of Makronisos was an islet before it joined the coast. It is a part of land that looks like a fish tail when seen from above. This is where the Necropolis is.

The Necropolis of Makronisos dates to the Hellenistic and Roman times and testifies to the existence of an ancient settlement in the region. Historical sources claim of the existence of the ancient settlement of Thronon as well as other smaller settlements somewhere in Ayia Napa which existed until the Early Christian period and were abandoned by the 7th century due to Arab raids.

The excavated tombs of Makronisos Necropolis are almost identical. Each tomb has a small carved pathway with steps that leads towards a rectangular underground entrance. The entrances were closed with a large rock plate or two small ones. The tombs seem to have had space for up to five burials.

The dead was placed on clay sarcophagi covered with three levels of tiles. The identical architecture of the tombs suggests that there was no class differentiation among the dead.  However, the funeral gifts and the fact that some of the clay sarcophagi were domestic and some were imported may bear witness to class differentiation.

Moreover, the potteries found inside the tombs along with the study of clay sarcophagi make evidence the trade relations of Cyprus with countries of the Middle East. Also, the funerary architecture, as well as the burning of the dead found on the surface of the nearby roads, show influence by the Hellenic funeral customs. This is similar to other Necropolises in Cyprus such as those in Salamina and Paphos.

In addition, remainders of a small ancient alter of the Cypro-classic and Hellenistic period were found near the archaeological site of Makronisos.

Even though some of the tombs in the Necropolis were looted by tomb raiders, and others were damaged by an ancient quarry operation near the cemetery, the few surviving tombs provide enough evidence for the development of settlements in the area. Today, some of the funeral gifts and one of the salvaged clay sarcophagi are on display at the Thalassa Museum in Ayia Napa.