Two local residents have raised the flags ahead of the US presidential hopeful's visit to Scotland later this week.
They said they wanted to "show solidarity" with the people of Mexico.
It comes after Mr Trump outlined plans to build a wall along the US-Mexico border to stop illegal immigrants.
Trump International Golf Links was opened by the businessman in 2012, after a lengthy battle with local people and environmentalists.
One of the flags has been raised by Michael Forbes, who refused to sell his land on the Menie Estate to Mr Trump before the course opened.
A second flag is being flown alongside a Saltire by David Milne, who lives in a former coastguard station overlooking the 18-hole course.
Mr Trump will return to Scotland on Friday to officially open the revamped Turnberry course in Ayrshire, which he also owns.
He is also expected to visit the Aberdeenshire course during his trip to Scotland.
Mr Milne said: "I am currently flying a Mexican flag along with my usual Saltire just for solidarity along with those worldwide who Trump has decried, insulted and threatened over the years, and will continue to decry, insult and threaten."
He said there were no plans to hold a protest during Mr Trump's visit.
"We don't think he's worth the effort," he said.
But he said the flag would be visible from the clubhouse.
"It's just enough to remind him that where he tried to drive us out he failed completely on that front."
Mexican flags are flying on properties surrounding the controversial Aberdeenshire golf course owned by Donald Trump.