The firm said it found the bitcoins - worth around $116m (£70m) - in an old digital wallet from 2011.
That brings the total number of bitcoins the firm lost down to 650,000 from 850,000.
MtGox, formerly the world's largest bitcoin exchange, filed for bankruptcy in February, after it said it lost thousands of bitcoins to hackers.
"MtGox had certain old-format wallets which were used in the past and which, MtGox thought, no longer held any bitcoins," said Mt Gox chief executive Mark Karpeles in the filing.
However, "on March 7, 2014, MtGox confirmed that an old-format wallet which was used prior to June 2011 held a balance of approximately 200,000 bitcoins," he said.This is a bit of good news for MtGox's creditors, who previously were facing the prospect that almost all of MtGox's bitcoins had been stolen. But it casts even more doubt on how MtGox was running its business, since MtGox was apparently able to lose track of 200,000 bitcoins. This, on top of earlier revelations that MtGox continued to allow bitcoin trades when it knew that it did not have enough bitcoins to give back to their customers, makes MtGox a cautionary tale of just how much can go wrong in the world of bitcoin exchanges.