Amnesty International Hong Kong deplored the arrests as "an outrageous assault on the rights to freedom of expression and peaceful assembly" and called for their release. They also are arresting people for protests earlier this summer, a step they said was a natural development as investigations were completed.
The sweep comes after a major rally planned for Saturday was banned by police on security grounds, and then called off by the organisers.
Wong was arrested at around 7:30 a.m. Friday en route to the South Horizons MTR station, according to the social network account of his group Demosisto. Police have not announced charges.
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.
Cathay sacked several staff over the protests and on Friday the airline went further, threatening to sack any staff who join a scheduled two-day strike next week. Wong faces separate charges of organizing the demonstration.
Chan, a founder of the pro-independence Hong Kong National Party that was banned last September, was arrested at Hong Kong's global airport yesterday on suspicion of "participating in riots" and "attacking police" during a protest on July 13, police said.
Activist Joshua Wong was arrested Friday morning while walking to a subway station, just hours after activist Andy Chan was arrested Thursday night at Hong Kong's airport, according to the Associated Press.
Demosisto is not a leader of this year's movement, which describes itself as "leaderless", though Wong has spoken out regularly in support of the demonstrations.
Wong's pro-democracy group, Demosisto, said the arrests were an attempt to scapegoat individuals in a movement that has built momentum without public figureheads. In 2047, though, Hong Kong's quasi-independent government will be dissolved and it will become fully absorbed into mainland China.
A website with ties to the Chinese communist party posted this clip of practice drills in nearby Shenzhen.
"We appeal to the public not to be afraid of political violence and white terror and continue to fight for their rights".
Also Friday, the Civil Human Rights Front - the organizer of the biggest recent demonstrations - said it was forced to cancel a rally to mark the fifth anniversary of an election edict from Beijing that sparked the 2014 Occupy protests after police withheld approval.
Hong Kong's crisis-hit government has refused to back down over the protests, which have by turns seen millions march, closed the airport and left city streets strewn with bricks and shrouded in tear gas. It would have marked the 13th consecutive weekend of protests had it gone ahead. "That's our first priority", said Bonnie Leung, a leader of the group.
In a statement responding to Reuters, Lam's office said her government had made efforts to address protesters' concerns, but did not comment directly on whether it had made such a proposal to Beijing, or received instructions.
"They arrested Joshua Wong and Agnes Chow this morning so there is a real danger we could face the same consequences as well". Jimmy Sham was not hurt but his friend required hospital treatment for an arm injury.
Critics claim the bill undermines Hong Kong's legal autonomy and puts the inhabitants and visitors of the country at risk of political prosecution by Beijing.
The protests began as rallies against a controversial extradition bill - now suspended - which would have allowed criminal suspects to be sent to mainland China for trial.