The oldest citing of the fortress belongs to Plinius Secundus (1st century AD). In the 2nd century AD it was a well-fortified Roman city in Colchis. It later fell under Byzantine influence. The name "Gonio" is first attested in Michael Panaretos in the 14th century. There's was also a short-lived Genoese trade factory there. In 1547 Gonio was taken by Ottomans, who held it until 1878, when, via the San-Stephano Treaty, Adjara became part of the Russian empire. The town was also known for its theater and hippodrome.
Additionally, the grave of Saint Matthias, one of the twelve apostles is speculated to be in Gonio fortress. However, the Georgian government currently prohibits digging near the gravesite. Other archaeological excavations are taking place on the grounds of the fortress, focusing on Roman times.
Gonio is currently experiencing a tourism boom. Most tourists come from Tbilisi in the summer months to enjoy beaches that are generally regarded as cleaner than Batumi's beaches (located 15km to the north).