The town of Mahates was founded on April 17, 1533 by Spanish conquistador Pedro de Heredia.

The municipality of Mahates also covers the village of Palenque de San Basilio, inhabited mainly by Afro-Colombians which are direct descendants of African slaves brought by the Spanish during the Colonization of the Americas and have preserved their ancestral traditions.

In 2005 the Palenque de San Basilio village was proclaimed Masterpiece of the Oral and Intangible Heritage of Humanity by UNESCO.

Due to its rapid increase on population Mahates quickly became a village and political chiefdom of the municipality and First Instance Court until the end of the 19th century.

In the village of San Basilio de Palenque the majority of its inhabitants are moreno (dark-skinned) Afro-Colombians who still preserve customs and from their African ancestors as well as their creole language, Palenquero.