Baggio Leung and Yau Wai-ching were arrested at their apartments today morning and are to be charged with "illegal assembly", according to the Facebook page of their party, Youngspiration.
They belong to a new movement calling for a complete split from China for semi-autonomous Hong Kong as concerns grow that the city's freedoms are under threat.
The calls for independence grew out of the failure of the mass Umbrella Movement rallies in 2014 to secure political reform and have infuriated Beijing.
The crackdown comes less than four months ahead of an expected visit by China's president Xi Jinping to mark the 20th anniversary of the handover of the city by Britain back to China in 1997 on July 1.
The charge against Yau and Baggio relates to them trying to barge in to a legislative council meeting in November after they had been barred, according to Yau's Facebook page.
Police did not provide immediate comments.
Despite being elected by the public in local elections, the pair were never allowed to take up their seats after protesting at their swearing-in ceremony last October.
They deliberately misread their oaths of office, inserted expletives and draped themselves with "Hong Kong is not China" flags.
Beijing intervened to ensure they were not given the chance to retake their oaths by making a special "interpretation" of Hong Kong's mini-constitution.
The ruling said that any oath taker who does not follow the prescribed wording of the pledge, "or takes the oath in a manner which is not sincere or not solemn", should be disqualified.
That move was heavily criticised by pro-democracy activists and legal experts as a massive blow to Hong Kong's judicial independence and sparked demonstrations by both pro- Beijing and pro-independence groups.
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