Hacienda Chichen dates from the 16th century, when it operated under the colonial system of encomiendas as a ranch and corn plantation. After Mexico's Independence, the haciendas came under ownership of the families holding the encomiendas, many of whom lived in Merida and owned more than one hacienda. As the demand for sisal grew, the haciendas established large plantations and controlled the production and export of sisal.

Typically, such estates would be an almost self-contained, socio-economic entity and would include a main house called 'el Casco' with its main well or noria, a Catholic chapel, jail and housing for farmers. Stone walls marked the boundaries and, at the main entrance, an elaborate arched gate served as a symbol of the landlord's wealth.

Many of these features can be seen, beautifully restored, at Hacienda Chichen. Well worth a visit are the fine arched gate, the noria, and the enchanting chapel, which can still be used for services.

In the early 20th century, the hacienda became the home of Edward Thompson, archaeologist and Vice-Consul of the United States, who was responsible for the re-discovery of the temples and pyramids of Chichen Itza. Thompson also lead the controversial dredging of the sacred cenote, where many important relics and human bones were discovered.

In 1923 the Carnegie Institute established its Maya Archaeological Expedition headquarters at the Hacienda, and rustic cottages were built in the grounds to house the archaeologists and research teams. These cottages were much later redeveloped as today's guest accommodations. Thompson's plant collection, supplemented by the Institute over a period of years, became the foundation for the beautiful gardens that surround the hotel buildings. Many of the towering palms, fruit trees and flowering shrubs that create such a delightful setting were originally planted in these early days of discovery.