Kottapuram was a part of
Muziris, the ancient port of Kodungallur and hence has a history as old as Muziris. Most of the traders of the ancient times were based on the fort, probably because it was surrounded by rivers on all three sides and had the landscape needed to become an early small port by sea. Rivers that are deep and shallow enough to enter from the sea was close to the lake. It can be seen that the Romans and the Greeks had trade relations even before Christ. They mainly bought pepper from Kerala. For the first time in India, Jewish immigrants reached Kerala through Kottapuram. Their first habitat was Mala, east of the fort. Muslims also reached Kodungallur through Kottapuram. The first muslim mosque in India was built 3 kilometers north of Kottapuram by
Malik Ibn Dinar. In AD 345, many Syrians came here under the leadership of the Babylonian merchant Knai Thomas. They also built churches and businesses here. There is a monument erected by the Archdiocese of Kottayam at the place where he is believed to have come.
Fortaleza da São Tomé, known locally as Kottappuram Fort/Tipu's Fort, was constructed in Kodungallur by Portuguese in 1523. The fort was enlarged in 1565, and passed into the hands of the Dutch in 1663 who destroyed the fort. Kottapuram Fort was an important part of the
Nedumkotta fort built by Travancore under the leadership of
Eustachius Benedictus de Lenoy to defend Tipu Sultan. ==Etymology==