Ernesto Robles, chief of police in the municipality of Chapala, identified the victims as a 72-year-old woman and an 84-year-old man, both from the Canadian province of Ontario. No names were released.
The couple arrived in Ajijic, a town popular with foreigner retirees, some six months ago, Robles said.
"The gardener arrived in the morning and found the door to the home open," Robles said.
"He went inside, and in the living room he found two bodies with various lesions. The home had been looted."
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Ajijic is a bucolic lakeside town som 50 kilometres south of the state capital Guadalajara, Mexico's second most populous city.
Some 5,000 foreigners, mostly US retirees, live in the town, according to municipal officials.
Immigration authorities and the state prosecutors are also investigating the case, Robles said.