Muharraq's origins are ancient, going back to the time of Dilmun some 5,000 years ago, but it came to prominence in the historical records during the era of Tylos when Bahrain came under domination of the Selucid Greeks, and Muharraq was the centre of a pagan cult dedicated to the shark god, Awal. The city's inhabitants, who depended upon seafaring and trade for their livelihood, worshipped Awal in the form of a large statue of a shark located in the city.
By the 5th century AD, Muharraq had become a major centre of Nestorian Christianity, which had come to dominate the southern shores of the Persian Gulf. As a sect, the Nestorians were often persecuted as heretics by the Byzantine Empire, but Bahrain was outside the Empire's control offering safety. The names of several of Muharraq's villages today reflect this Christian legacy, with Al-Dair meaning 'the monastery' and Qalali meaning a 'monk's cloisters'