The Youbit exchange said it had lost 17 percent of its assets in the attack today.
It came eight months after nearly 4,000 bitcoin -- then valued at 5.5 billion won ($5 million) and nearly 40 percent of the exchange's total assets -- were stolen in a cyber attack blamed on North Korea.
"We will close all trades, suspend all deposits or withdrawals and take steps for bankruptcy," the exchange said in a statement which did not assign blame for the latest attack.
The exchange -- founded in 2013 -- brokered trades of multiple virtual currencies including bitcoin and ethereum.
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Investing in virtual currencies has become hugely popular in the hyper-wired South, whose trades account for some 20 percent of global bitcoin transactions.
About one million South Koreans, many of them small-time investors, are estimated to own bitcoin. Demand is so high that prices for the unit are around 20 percent higher than in the US, its biggest market.
Concerns over a potential bubble have unnerved Seoul's financial regulators, who last week banned its financial institutions from dealing in virtual currencies.
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