Kodungallur is situated on the west coast and was once a great port of the Chera rulers. Kodungallur was a critical trade link in Indian Ancient Maritime History. It was known as Muziris to Pliny the Elder (N.H. 6.26) who describes it as primum emorium Indiae.
The port was familiar to the author of the Periplus of the Erythraean Sea who described it as being situated on Pseudostomos river (Greek for "false mouth" - a precise translation of the Malayalam description of the mouth of the Periyar, Alimukam) two miles from its mouth
Studies by the archaeologist Dr. K.P. Shajan and his associate V. Selvakumar of the Centre for Heritage Studies, have unearthed the clues to this ancient port at a place called "Pattanam" (meaning 'The city' in Malayalam) around 10 km from Kodungallur. Among the many things unearthed are Roman amphora pieces, West Asian pottery (200 BC - 700 AD), Chinese Pottery (1700 AD), Rouletted Ware and copper coins. They also excavated a boat made of a single wood which gives the indications that the place was an erstwhile shore. The radio carbon dating shows the age of the boat to be approximately 2500 years. The brick structure excavated is a clear indication of early human settlement in this area.

Muziris, near the tip of India, in the Peutinger Table.
The ancient Greek explorer, Hippalus landed at this port after discovering the patterns of the Indian monsoon trade winds on his way from the East coast of Africa. The evidence of the Peutinger Table suggests that there was a temple to the Roman emperor Augustus.
The Greeks, the Romans (known locally as the Yavanas), and the Jews all have come to this place at different times in its ancient history.
Roman gold and silver coins bearing impressions of Roman Emperors Tiberius and Nero were discovered in the village of Parur near the town during 2000.
A second-century papyrus from Egypt concerning the transshipment of goods originating in Muziris from the Red Sea to Alexandria attests to the continued importance of the port in the Indian Ocean commerce a century after Pliny and the Periplus.
Thomas the Apostle of Jesus with his followers is believed to have landed in Cranganore in the year AD 52 and preached the gospel. It thus became the earliest Nasrani Syrian Christian centre of Malabar; monuments built in the memory of Thomas still exist. The existence of a thriving Christian Community here attracted the attention of others and the Bishops who came from Persia chose this place for their residence. The bones of the right hand of St Thomas were placed as a memento.
Malik Ibn Dinar and 20 others who were the followers of Prophet Muhammad, the founder of Islam, first landed here when they came to India. Islam received royal patronage in some states here, and later spread to other parts of India. He built a mosque there in the shape of a Hindu temple. It could also have been the first mosque in the Indian subcontinent as the exact date of making is not known but is believed to be in 629 AD. Though, generally it is considered to be the second mosque of the world after the mosque in Medina,Saudi Arabia

The Syrian Church was firmly established here before the 9th century. In fact the Jews' settlement in Kodungallur was still earlier. The latter, claimed to hold grants dated A.D. 378. The cruelty of the Portuguese drove most of the Jews to Cochin[citation needed]. Up to 1314, when the Vypin harbour was formed, the only opening in the Cochin backwater, and outlet for the Periyar, was at Kodungalur, which must then have been the best harbour on the coast. In 1502 the Syrian Christians invoked the protection of the Portuguese. With the influence of Portuguese, most of the Syrian Christians accepted Latin Rite in Kodungallur. Kodungallur was erected as an Archdiocese in 1609 but was annexed to the Vicariate of Verapoly in 1838 and further in 1886 the diocese itself was suppressed. In 1987 Archdiocese of Verapoly was bifurcated and the Diocese of Kottapuram was formed. Catholics in Kodungallur today belong to this diocese.

In 1523 Portuguese built their first fort there, and in 1565 enlarged it.

In 1661 the Dutch took the fort, the possession of which for the next forty years was contested between this nation, the zamorin, and the raja of Kodungalur. In 1776, Tipu Sultan seized the stronghold. The Dutch recaptured it two years later, and, having ceded it to Tipu Sultan in 1784, sold it to the Travancore raja, and again in 1789 to Tippoo, who destroyed it in the following year.
After Tipu's death, The Kodungallur Kovilakam controlled the lands of Kodungallur. Kodungallur then formed an autonomous principality subordinate to the Raja of Cochin and remained thus until Indian Independence in 1947. The Kodungallur Kovilakam was renowned as a centre of learning during this period. Scholars from all over Kerala came to live in the palaces and study Sanskrit and Vedic science.
Flood of 1341
The flood of the river Periyar in 1341 AD resulted in the splitting of the left branch of the river into two just before Aluva. The flood silted the right branch (known as River Changala) and the natural harbour at the mouth of the river, and resulted in the