The raids were conducted on the premises of buysellbit.Co.In in Bopal area of the city and rbi.Rbit.Co.In in Satellite area of the city yesterday, officials said.
The raid continued today as well and the ED has found records of bitcoins transactions.
The move comes after the Reserve Bank of India (RBI) issued an advisory cautioning general public against the use of bitcoins.
Bitcoin is a virtual currency that can be generated through complex computer software systems with solutions shared on a network, although the process is complex and such 'mining' can be done only on very powerful servers.
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RBI is yet to come out with a clear regulatory framework for bitcoins, which have been gaining currency across the world over the past few months.
An ED official said that many transactions were recorded on buysellbit.Co.In, owned by Mahin Gupta and officials are checking whether these are cross-border transactions or internal transactions. Gupta was also grilled.
"We are tracking the people who availed these services and from whom they availed these services," the official said.
The premises of rbi.Rbit.Co.In, owned by Nilam Doctor, were sealed, sources said.