The site is considered to have two stages. One is called Ñudee, which is the original Mixtec name for Huajuapan and means "place of the brave," and covers the era between 400 BCE and 250 CE. The other is called Nuiñe and covers the time period between 250 and 800 CE. Artifacts here show that during both periods, this settlement had strong ties with other Mixtec settlements in other parts of modern-day Oaxaca. The area began to decline after 800 CE, possibly due to military pressure from lords in other regions. The region would not grow again until the Spanish established their city here in the 16th century.