According to the Popol Vuh, the Título de Sacapulas, and other sixteenth-century Chronicles, the lords of the Tz'ikinjay or "Bird-House" nation or Amaq' who founded the Tz'utujil state did not come to the region until the Late Postclassic period.

In Pre-Columbian times, the Tz'utujil nation's capital was a town near Santiago Atitlán known both as Chiya' ("At the Water") and by the name of the ruling chinamit, "Tzikinjaay," which was conquered in 1523 by the Spanish conquistador, Pedro de Alvarado, with the help of the nearby Kaqchikel.

[7] The site of the ruins of the old capital, located atop a lake-front hill at the base of Volcán San Pedro, just west of Santiago Atitlán across a narrow inlet, has been known for centuries as Chuitinamit, "the walled-town above."

It is noteworthy that the original Proyecto Lingüístico Francisco Marroquín team that worked to document Tzutujil in the 1970s included at least two native-speakers from San Juan, alongside at least two from Santiago Atitlán.

The Testamento Ajpopoljay, the only colonial titulo written in the Tz'utujil language known to have survived to the twentieth century, was authored by a Juanero named Jerónimo Mendosa in 1569 and was later presented by his descendants to the Spanish colonial government as part of San Juan's land titles in 1640, during a dispute over land invasions by K'iche' people from Santa Clara La Laguna and Santa Catarina Ixtahuacan.

[8] Although Guatemalan scholar Mario Crespo M. published an analysis of the document's contents based on a line-by-line preliminary translation of it sometime before 1968, it does not appear that he or anyone else transcribed the actual Tz'utujil text.

The Guatemalan Civil War was fought between government forces and leftist rebels, the Revolutionary Organization of the People in Arms (ORPA) (Spanish: Organización Revolucionario del Pueblo en Armas).