Wong, pro-independence activist Agnes Chow and campaigner Andy Chan are seen as key figureheads of anti-government movements in Hong Kong over recent years, reports the South China Morning Post.
According to a police source, Wong and Chow were arrested on Friday morning for unlawful assembly in relation to the siege of police headquarters in Wan Chai by thousands of protesters on June 21, when demonstrators demanded a complete withdrawal of the now-shelved extradition bill and an exoneration of those arrested in previous clashes.
A third member of the party Ivan Lam, who was also accused of taking part in an unauthorised assembly, was said to be out of town.
Wong, who served time in jail for his role in the 2014 Occupy movement, was detained early on Friday on his way to a metro station, according to the pro-democracy Demosisto party of which he is secretary-general.
A police source said Chow was arrested at her home in Tai Po.
Both are being held for questioning at police headquarters in Wan Chai.
Meanwhile, Chan was arrested on suspicion of rioting and assaulting a police officer on Thursday night after he was stopped from boarding a plane at the Hong Kong International Airport.
Chan confirmed his arrest on a Facebook post.
The arrests come after the police earlier this week, rejected the Civil Human Rights Front's plan to march from Central to Beijing's liaison office in Sai Ying Pun on Saturday, reports the South China Morning Post.
The Front is behind the biggest marches held in Hong Kong since the eruption of the political crisis in early June, sparked by the now-abandoned extradition bill, which would have allowed criminal suspects to be sent back to mainland China.
Speaking on a radio programme on Friday, the Front's convenor Jimmy Sham said if they lost their appeal, the march would be postponed.
"The front can only apply for another date for a march. We will not organise an unlawful march," he said.
The anti-government movement has five main demands, including the bill's complete withdrawal, the establishment of an independent inquiry into police's handling of protests and genuine universal suffrage.
( With inputs from IANS )