“In short, this man gave two billion rubles of his own money and they decided to abuse him,” said Mikhail Gelfand, a Russian biologist who had taught courses for Dynasty. “Dynasty formed around itself a community of successful and respectable people. Apparently that was seen by the government as something suspicious and dangerous.”

Officially, the cause was Dynasty’s support for the organization Liberal Mission, which held lectures on modern politics last year in Moscow, and the foreign money was Mr. Zimin’s own, from offshore banks. But Mr. Zimin, who has been cautiously critical of the government, has also been criticized on state television, which aired what was described as an exposé accusing his son of financing political parties opposed to Mr. Putin. Mr. Zimin’s social media accounts were hacked in late May.

Dynasty has provided a lifeline for many scientists in Russia for the past 13 years.

Sergey Popov, an astrophysicist, was finishing a postdoctoral degree in Italy in 2003 and considering his next step. He was hesitant to return to Russia, where scientists’ salaries were low and the political situation uncertain. Dynasty offered Mr. Popov a fellowship that he said persuaded him to return. “It wasn’t enough to live on,” he said recently in a telephone interview. “But just enough to get by, to rent an apartment in Moscow for instance.”

For one month, Dynasty’s board wrestled with a question pondered by many organizations now: Should it continue to work despite the foreign-agent label? Even as consultations with lawyers continued, the Justice Ministry fined Dynasty more than $5,000 for having failed to voluntarily register as a foreign agent.

Finally, at a meeting last Sunday in Montenegro, the board voted unanimously to close.

“In principle, yes, an organization can continue to function as a foreign agent,” said Sergei Guriev, a Russian economist and Dynasty board member who led that meeting. “But it is clear that the organization cannot continue to function without problems for our stakeholders.” Mr. Guriev left Russia in 2013, fearing he would be persecuted because of his liberal political views.