San Andrés was an important site during the Late Pre-Classical period, from 400 BC to AD 25. In the Late Classical period, AD 600 to AD 900, the site was considered a main regional Mayan hub that oversaw the lesser settlements of the Zapotitán Valley. In this period, San Andrés maintained strong ties with the Kingdom of Copán, whose cultural and political influence spread across western and central El Salvador, evidenced by offerings of flint scepters, Copador ceramics, and jars with Mayan text. The original footprint of this monumental location was likely around 200 hectares, and it is surrounded by 350 archaeological sites, including Joya de Cerén. The total population of the Zapotitán Valley in the Late Classical period likely ranged from 40,000 to 100,000 people.
A monument known as the acropolis sits at the heart of San Andrés: an elevated surface built with clear architectural influences from the outlying Mayan areas. The acropolis is surrounded by terraces and market plazas; rooms and residence structures for the noble families are located closer to the temples. Communities of Mayan artisans such as Joya de Cerén also dot the area. These settlements specialized in ceramics, obsidian, jades, and pigments made from cinnabar (mercury oxide) and hematite (iron oxide).
There was also an important settlement in San Andrés in the colonial period, as revealed by the indigo pit for dye extraction that was in use in the 17th century (1650-1660), on one of the Dominican Estates in San Salvador. The San Andrés archaeological site has a local museum, shops, and an amphitheater for visitors to explore.