MANILA, Jul. 1 (Reuters) - The Philippines' dominant Marcos and Duterte political dynasties, uneasy allies for two years, are gearing up for an election showdown that could upset policy stability in the Southeast Asian nation in the coming years.

Vice President Sara Duterte's resignation as education minister in President Ferdinand Marcos Jr's cabinet was followed on Tuesday by her bombshell announcement that her father, ex-President Rodrigo Duterte, and two brothers would run for the Senate next year.

The collapse of the alliance had long been expected, but the political challenges by the Duterte men could upset Marcos' hopes of consolidating power so he can groom a potential successor for 2028, when analysts say Sara Duterte may seek the top job. Philippine presidents are limited to a single six-year term.

"It is a threat," said Jean Encinas-Franco, a University of the Philippines political science professor. "It is a message to the Marcoses as it is a message to the Filipino people that 'we are alive and kicking'."

Marcos, 66, shrugged off the Dutertes' plans, telling reporters on Thursday, "It's a free country. They're allowed to do whatever they want."

It is unclear how the potential candidacies by Duterte, 79, and his sons - they would not file for the Senate races until October - might affect policy in the near term. But victories in the May midterm elections by the Duterte family, backed by their strong political base, could complicate Marcos' efforts to pass laws that diverge from the Dutertes' interests.

The former president may be motivated to run for "political protection", said Manila-based political analyst Julio Amador. Duterte is being investigated by the International Criminal Court (ICC) over his signature "war on drugs" campaign, where thousands were gunned down in what authorities called vigilante killings during his 2016-2022 presidency.

Harry Roque, his spokesperson when he was president, dismissed the suggestion, saying the court has no jurisdiction over the Philippines.

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