Chile and Peru have traditionally had a dismal relationship, dating back to the late 19th century when they fought a war in which Chile annexed a slice of Peruvian land.
They are currently in dispute at The Hague over their maritime border, and Peru's new President-elect Ollanta Humala has a history of making scathing comments about the Chileans.
But Markarian, a Uruguayan who used to coach in Chile, said history and political rivalry should not be allowed to spoil Tuesday's Group C clash in Mendoza.
"They're two countries that I love a great deal - Peru where I'm working very happily, and Chile, where I was very well treated and where I still have many friends," he said after a training session in Mendoza.
"Please, let's not mix things. Let's allow this to be a football match and let's enjoy it as much as possible.
"I've asked my players to be careful with what they say to the press, I've seen a few strange headlines that I haven't liked. I want this to be nothing more than a purely footballing encounter."
Markarian's words were echoed by Peruvian defender Renzo Revoredo, who appealed to both sets of fans for mutual respect.
"It's a football match - an important one but a football match nonetheless," he said.
Chile and Peru are level on four points at the top of Group C. Uruguay (2 points) and Mexico (0 points) are the other two teams in the group.
Around 30,000 Chileans have made the short trip across the Andes to Mendoza to support their team and will vastly outnumber the Peruvian fans in the ground.
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