It is believed that El Niño began after oceanic changes which occurred 5000 years before present, resulting in a change in ocean circulation along the coastline of Peru. There are also theories held by some which state that El Niño has existed as a climate factor on earth for much longer than that. An interesting comment was made by Ellen Thomas who thought that it would be difficult for El Niño to have existed while the Panama canal was open for deep circulation. If the Pacific ocean was like a bath tub full of water, it would be pretty hard to maintain the sloshing of water in the bath tub or an ocean circulation, if there was a hole in the side, like the open Panama canal before the late Miocene.

(Taken from www.carleton.ca)