The village was first mentioned as "the old castle of Konteas" in a census document of the Great Lavra monastery, of which it was a dependency. This castle had probably been built during the Venetian rule of the island. According to local legends, the village was originally located near the sea, and it was resettled to the present inland location due to pirate raids. The original location was probably the small port of Agios Giannis, where ruins of a castle still remain.
Ottoman period
The bay of Kontias was mentioned by the Turkish naval sailor Piri Reis in 1521 as "Qondia Körfezi". Ships awaited favourable conditions to enter the Hellespont straits there. Piri Reis mentioned a castle at the bay, but no village. In the following ages, the port was mentioned by several travellers in the area. In 1770, during the Orlov Revolt, part of the Russian Navy fleet anchored in the port of Kontias, when they besieged Myrina. The first mention of the village in the present location was in 1785, by Choiseul-Gouffier. Kontias was an organized settlement and one of the largest villages on the island. In 1856 it had 290 men who paid 9,280 piatres to avoid conscription. It had 176 families in 1863, and 187 in 1874. In the same year the municipality of Kontias was mentioned, consisting of the villages Kontias, Tsimandria, Portianou, Agkariones, Pesperago, Sarpi and Livadochori. This corresponds with the present municipal unit Nea Koutali. It was a rich village, because besides the agricultural activities there were many sailors and shipowners, including Papagiannis with 60 boats. The village school was first mentioned in 1873. A new school building was built in 1880. In 1910 two fountains were built: Tsikoulas and Kali Vrysi.
Modern period
Kontias joined the rest of Greece after the Balkan Wars in 1913. It became an independent community in 1918 named Kondias, which was changed into Kontias in 1940. During the years between the world wars, it had a remarkable growth in economy and population. In 1920 it had 1,272 inhabitants, making it the third largest village in Lemnos. In 1940 it had 1,500 inhabitants, making it the second village in population, after Myrina. A refugee settlement was built in 1926. Cotton production on Lemnos began from Kontias. After World War II, the population decreased due to internal and external migration. The population was 551 in 1991.