Activists among the fractious opposition groups said they had made steps towards agreeing a common position among themselves but failed to make any headway in discussions with representatives of the Assad regime.
"The chances were missed," said opposition figure Samir Aita said at a press conference.
"By the end of the meeting the majority of the opposition from Damascus were disappointed that we didn't achieve any results."
There was little hope for the talks in Moscow -- which kicked off Monday -- given the absence of main Western-backed exiled Syrian opposition National Coalition from the talks.
The meeting in Moscow -- which followed a similar round of fruitless talks here in January -- was seen by analysts as a way for Russia, a key backer of Assad, to bolster its influence in the region.
The opposition National Coalition accused Russia of seeking to use the talks to shore up Assad, and declined to attend. It has been increasingly sidelined by powerful regional actors such as Saudi Arabia and Egypt.
Most of Syria's opposition in exile has made it clear that Assad must step down in any deal to end the conflict that began with demonstrations against his rule in March 2011.
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