Meeting in the city's Victoria Park, some chanted slogans such as "End one party rule" and "Democracy for China now" as they skirted an unprecedented prohibition on the annual vigil justified by police due to the coronavirus crisis.
The anniversary has struck an especially sensitive nerve in the former British-ruled city this year after China's move last month to impose national security legislation and the passage of a bill outlawing disrespect of China's national anthem.
It also comes as Chinese media and some Beijing officials voice support for protests in the United States against police brutality. The crackdown is not officially commemorated in mainland China, where the topic is taboo and discussion censored.
In Hong Kong, which just reported its first locally transmitted coronavirus cases in weeks, police had said a mass gathering would undermine public health. But several thousand made it to Victoria Park where they held a minute of silence.
Elsewhere around the city, Hong Kongers took to the streets and also lit candles in other peaceful rallies.