One of the notable aspects of Chan Santa Cruz was the development of a new religion, sometimes called "the cult of the Talking Cross". This was actually mostly an adaptation of Roman Catholicism and native folk beliefs to the circumstances of the war which cut the Maya off from the Yucatán's Hispanic population. As no native Maya had been ordained as priests at the time, the village lay assistants maestro cantores were promoted to the priesthood by the authority of the Chan Santa Cruz leaders, who in turn were said to get their authority directly from God who talked to them through a wooden cross kept in a sanctuary in the town's church.
The town was founded in 1850 near a cenote, a natural well providing a year round source of drinking water, where the talking cross was said to have been found.
From the late 1850s through 1893 the United Kingdom recognized Chan Santa Cruz as a de facto independent nation. This was largely due to Chan Santa Cruz's trade relations to the British colony of British Honduras, and the fact that the Cruzob army was substantially larger than the garrison and militia in British Honduras. The British found it both practical and profitable to maintain good relations with Chan Santa Cruz.
Chan Santa Cruz was conquered by the Mexican army in the early years of the 20th century. The shrines of the "Talking crosses" still have some local worshipers.