The exchange of both text and voice messages is being considered, although the source stressed that details of the pact are still being finalised. The two companies are planning to announce the deal on Wednesday in the US, the source said.
A Microsoft representative declined to comment on the matter. A Yahoo representative was not immediately available for comment.
The three major IM providers -- Yahoo, Microsoft and AOL -- have talked about interoperability for some time, but there has been only limited progress.
For some months now, workers at businesses running Microsoft's Live Communications Server have been able to exchange text messages across multiple instant messaging programs. However, consumers have had to manage multiple accounts in order to use more than one of the big three services: AOL Instant Messenger, Yahoo Messenger and MSN Messenger.
Third-party programs like Trillian have allowed users to connect to multiple services within a single program.
Details of the Yahoo-Microsoft agreement were reported earlier by the Wall Street Journal.
CNET News.com's Alorie Gilbert contributed to this report.
