Crowds streamed into one of the city's main parks that has hosted huge Tiananmen anniversary vigils for the past three decades, with smaller rallies erupting across the finance hub.
Police arrested some demonstrators in a shopping district on although they allowed the main rally at Victoria Park to proceed.
The displays of resistance came hours after Hong Kong's legislature passed a bill criminalising insults to China's national anthem, which the pro-democracy movement sees as yet another example of eroding freedoms.
China's plans to impose a security law on Hong Kong criminalising treason and subversion, has cemented fears that the semi-autonomous city is losing its treasured liberties.
"I've come here for the vigil for 30 years in memory of the victims of the June 4 crackdown, but this year it is more significant to me," a 74-year-old man who gave his surname as Yip told AFP as he joined the crowds inside Victoria Park.
"Because Hong Kong is experiencing the same kind of repression from the same regime, just like what happened in Beijing."
Hundreds of people -- by some estimates more than a thousand -- were killed in 1989 when China's communist rulers deployed the military into Beijing's Tiananmen Square to crush a student-led movement for democratic reforms.
Commemorations of the event are forbidden in mainland China but have been allowed in semi-autonomous Hong Kong, which has been granted liberties under the terms of its 1997 handover from the British.
This year's vigil was banned, with authorities citing coronavirus restrictions on group gatherings.
However thousands of people, including prominent democracy leaders, poured into Victoria Park on Thursday evening and lit candles as an act of remembrance and resistance.
Some wore black t-shirts with the word "Truth" emblazoned in white. Others were in office attire.
Many shouted pro-democracy slogans including "Stand with Hong Kong" and "End one party rule", in reference to the communists who hold monopoly power in China.
Other candle-light vigils were held in local neighbourhoods, shopping districts and churches across Hong Kong, according to AFP reporters covering the various events.
- Neighbourhood, church vigils -
Crowds have swelled at Hong Kong's Tiananmen vigils whenever fears have spiked that Beijing is prematurely stamping out the city's own cherished freedoms, an issue that has dominated the finance hub for the past 12 months.
The city was engulfed by seven straight months of huge and often violent pro-democracy protests last year -- rallies that kicked off five days after the last annual vigil.
In response to those demonstrations Beijing last month announced plans to impose the security law.
China says the law -- which will bypass Hong Kong's legislature -- is needed to tackle "terrorism" and "separatism" in a restless city it now regards as a direct national security threat.
Critics, including many Western nations, fear it will bring mainland-style political oppression to a business hub.
- 'Complete nonsense' -In mainland China, authorities do not allow any open discussion about the Tiananmen crackdown and censors scrub any mention of it off the internet.
The candle emoji has been unavailable in recent days on China's Twitter-like Weibo platform.
Police in Beijing prevented an AFP photographer from entering Tiananmen Square to record the regular pre-dawn flag-raising ceremony on Thursday and ordered him to delete some photos.
The United States and Taiwan issued statements on Wednesday calling on China to atone for the deadly crackdown.
"Around the world, there are 365 days in a year. Yet in China, one of those days is purposely forgotten each year," Taiwan's President Tsai Ing-wen tweeted.
Secretary of State Mike Pompeo tweeted a photo of him meeting prominent Tiananmen survivors.
China's foreign ministry described calls for Beijing to apologise for the crackdown as "complete nonsense".
"The great achievements since the founding of new China over the past 70 or so years fully demonstrates that the developmental path China has chosen is completely correct," spokesman Zhao Lijian told reporters.