The Russian government says the USAID mission must close down by October after 20 years of offering assistance.
The Russian authorities have grown increasingly suspicious of non-governmental organizations (NGOs), says Steve Rosenberg, with the BBC in Moscow.
"There are a lot of people in power in Russia today who believe that the United States has been using grants to NGOs in Russia as a way of influencing what happens here, the political situation... and even to spark revolution," he says.
During its time there, USAID has spent more than $2 billion on a whole range of aid programs there, including fighting disease and help the environment. There are also many programs to develop democratic and civil society institutions, which Rosenberg says tend to be the most controversial.