Andy Chan, who founded the Hong Kong National Party in March, was banned by the city's government from taking part in the September poll.
But the party, which claims there is growing support for the semi-autonomous city to break away from mainland China, said it was "honoured" to be the first to have a candidate disqualified.
"The National Party on July 30 received an email from the government saying they have officially disqualified the party's convenor Andy Chan," a statement said today.
Chan was one of at least 13 pro-democracy candidates who refused to sign a form saying the city is an "inalienable" part of China.
Critics slammed the new stipulation as political censorship and an attempt to deter candidates from advocating self-determination or independence from Beijing, and campaigners have challenged the move in court.
Beijing and Hong Kong officials have repeatedly said that advocating independence goes against the city's mini constitution, known as the Basic Law, and that independence activists could face legal consequences.
"If a person advocates or promotes the independence of the HKSAR, he cannot possibly uphold the Basic Law or fulfil his duties as a legislator," it said.
Some young campaigners are calling for more distance or even a complete breakaway from the mainland as fears grow that freedoms in the semi-autonomous city are disappearing as Beijing's clout grows. Some activists say they are not afraid to use violence to achieve their goal.
But concerns have grown that such freedoms are now fading as Beijing increases its influence across a range of areas, from politics to the media.
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