Estonian police investigated the case with the FBI, and US authorities want to extradite the pair - Estonians Sergei Potapenko and Ivan Turogin.
A statement from the US Department of Justice (DoJ) says the pair are accused of wire fraud and conspiracy to commit money laundering - crimes punishable by up to 20 years in prison.
The defendants have appeared in court in the Estonian capital Tallinn and are being held pending extradition to the US, the statement says.
Giving details of the alleged scheme, the DoJ says the two defrauded victims by offering them the chance to buy into HashFlare's cryptocurrency mining operations.
Customers around the world are said to have purchased more than half a billion dollars' worth of HashFlare contracts from 2015 to 2019. But the operation allegedly overstated its capabilities.
The DoJ alleges that victims were also promised dividends if they invested in Polybius, a virtual bank Mr Potapenko and Mr Turogin said they had set up.
The defendants are said to have raised $25m this way - but no bank was ever formed.
It was "one of the largest fraud cases we've ever had in Estonia", he said on Monday, quoted by Estonia's ERR news agency.
The case comes at a time of heightened nervousness in the cryptocurrency market, following the collapse of the world's second-largest crypto exchange, FTX.