Hari Simran Singh Khalsa, born and raised in New York, had arrived in the colonial town of Tepoztlan for a yoga retreat with his wife Ad Purkh Kaur and yoga students on December 26.
His body was discovered in one of the ravines in the area around 2 pm on Friday, four days after he went hiking in the rugged mountains that surround the town.
The place where the body was found was not far from where Khalsa was last seen in a picture of himself that he sent his wife by cellphone.
The cause of death has not been ascertained yet and an autopsy will be conducted, officials said.
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The US Embassy in Mexico City confirmed the death, saying it was offering consular support to Khalsa's family and extended the American government's condolences, reports said.
The couple have been living in Leesburg, Virginia, but were planning to move back to New York.
Khalsa appears to have fallen while hiking and sustained a fatal injury to the head, the family said a statement.
Tepoztlan, a popular tourist destination near Mexico City, is known for its mountain peaks and the towering cliffs.