The cyclists — Holger Hagenbusch of Germany and Krzysztof Chmielewski of Poland — had been traveling the world by bicycle.
But after being reported missing by relatives, they were found dead at the foot of a sheer rock face in the Mexican state of Chiapas.
Investigators initially said the pair appeared to have lost control on a winding mountain road.
However, after a group of fellow cyclists questioned that version of events, a special prosecutor newly appointed to take over the case said the cyclists had in fact been murdered.
“It may have been an assault, because our investigations up to now indicate this was an intentional homicide,” special prosecutor Luis Alberto Sanchez told journalists.
The motive appears to have been robbery, he said.
Chmielewski sustained a head injury that may be a gunshot wound, he added.
Hagenbusch's brother Rainer, who flew to Mexico to identify him, wrote on his Facebook page that both bodies had been mutilated.
“The Polish cyclist was decapitated and had a foot missing,” he said.
The Chiapas state government vowed to “intensify the investigation” to solve the case.
Investigators say the two cyclists met in the town of San Cristobal de las Casas on April 20th and decided to travel together to the ancient Mayan ruins at Palenque, some 200 kilometers (130 miles) away.
Chmielewski's body was found on April 26th, and Hagenbusch's on May 4th.
Mexico is struggling to deal with a wave of violent crime that left a record 25,000 murder victims last year.
Since the government launched a controversial military offensive to fight the country's powerful drug cartels in 2006, the country has registered more than 200,000 homicides.