The Securities and Exchange Commission charged former cryptocurrency exchange BitFunder and its founder with fraud Wednesday.

The regulator alleged that BitFunder and founder Jon E. Montroll ran the operation as an "unregistered securities exchange" and defrauded users of that exchange, according to a SEC statement.

"Platforms that engage in the activity of a national securities exchange, regardless of whether that activity involves digital assets, tokens, or coins, must register with the SEC or operate pursuant to an exemption," Marc Berger, director of the SEC's New York Regional Office, said in a statement.

Montroll also failed to disclose a cyberattack on the exchange's system and a bitcoin theft that happened as a result, according to the SEC statement.

"We will continue to vigorously police conduct involving distributed ledger technology and ensure that bad actors who commit fraud in this space are held accountable," Lara S. Mehraban, Associate Regional Director of the SEC's New York Regional Office said in the statement.

The U.S. Attorney's Office for the Southern District of New York also filed a complaint against Montroll Wednesday for "perjury and obstruction of justice during the SEC's investigation," according to the statement.

A lawyer for Montroll couldn't immediately be reached.

BitFunder closed just a one year after its launch in December 2012. The site's shutdown followed the Global Bitcoin Stock Exchange shutdown in October 2012 and btct.co's shutdown in October 2013.

The charges highlight uncertainty surrounding whether or not bitcoin and other cryptocurrencies should be classified as securities. It's unclear whether the coins are utility tokens or securities that would fall under the SEC's oversight, and many start-ups have barred U.S. residents from officially participating in token sales as a result.

The regulator has stepped up its crackdown on cryptocurrency-related fraud in the last eight months, with a series of investor bulletins, stock trading suspensions and initial coin offering halts.

Just last Friday, the commission temporarily suspended trading in three tiny stocks due to questions about recent announcements involving blockchain and cryptocurrency investments. And in late January, the SEC halted and froze the assets of AriseBank, which claimed to have raised $600 million in the largest initial coin offering to date.

SEC Chairman Jay Clayton has also spoken out more about cryptocurrencies. He said earlier this month in a hearing before the Senate Banking Committee that federal financial agencies may ask Congress for increased legislation on cryptocurrency-related operations. He added that he is "not satisfied" when people think cryptocurrency trading platforms have the same protection as a stock exchange.

Bitcoin prices fell roughly 8 percent Wednesday, trading near $10,278 as of 3:42 pm ET.



— CNBC'S Evelyn Cheng contributed to this report.