Several thousand protesters including scientists and intellectuals took to the streets of Moscow to express fears that scientific research in Russia faces dire prospects due to stifling bureaucracy and mismanagement.
Prominent opposition figures including top activist Alexei Navalny joined the rally.
"Authorities are strangling science" and "Nobel laureates are foreign agents" read some of the placards held by protesters.
"Putin cannot solve problems, he is the problem," read another sign.
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The protest was originally called in support of a top private foundation whose 82-year-old founder, philanthropist Dmitry Zimin, has recently come under fire for financing Russian science from overseas accounts.
Discontent among scientists has been brewing for months but the crackdown against Zimin's Dynasty Foundation sparked acute anger and disbelief.
The justice ministry in late May added the Dynasty foundation, set up by ex-telecoms magnate Zimin, to its list of "foreign agents" under a law that critics say is designed to muzzle critics of President Vladimir Putin.
An AFP correspondent said more than 2,000 people turned out for the rally, while activists counted some 3,500 participants.
Antonina Aleksandrova, a biologist at a cancer treatment centre in Moscow, slammed the attack against Zimin's foundation.