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The name of Marsaxlokk is derived from the words meaning South East Harbour. When the Phoenicians traveled straight from Tyre and Sidon (modern) Lebanon), they used to enter into this safe harbour and travel to the place known as Tas-Silġ, where, among other important buildings archeologists discovered remains of a Temple dedicated to Astarte.

Little is known about this village during the Middle Ages. During the hey day of the Turkish Empire however, when its warriors used to land and attack Zejtun, the village was practically deserted because of the danger of being killed or captured and sold as slaves. But as the power of the Turkish Empire and pratical attacks diminished, the village began to grown gradually. Today this village has grown and developed into a tourist attraction, with its simple lifestyle.

The first time when population is mentioned was in 1890, numbering 210 souls. At first, this village was considered to be a summer resort and many people from towns and villages afar used to pass the three summer months. As time passed however, people came to stay the whole year round. According to the census of 1961, the population numbered 778. In the year 2006, the population rose to 3,200.