Apollonia became autonomous from Cyrene at latest by the time the area came within the power of Rome, when it was one of the five cities of the Libyan Pentapolis, growing in power until, in the 6th century AD, it became the capital of the Roman province of Libya Superior or Libya Pentapolitana.

The existence of buildings in the sea was noted by Beechey (1827), with some rough drawings, and Goodchild (1950s) and André Laronde also published archaeological surveys of the site.

The results of this work were published, complete with maps and diagrams of underwater buildings in the references cited below.

The Crete earthquake and tsunami of 21 July 365 AD apparently caused extensive damage to the city and harbor.

A marble inscription testifies to its use as a Roman military commander's house, however the identification of the name and status of the man who built the palace is problematic.