Did eBay steal confidential information from Craigslist to launch its own classifieds site? Craigslist says it did, and the classified ads company’s complaint is now being investigated by prosecutors with the Justice Department.

The spat goes back to 2004, when eBay purchased a 28 percent stake in Craigslist. Three years later, eBay launched an online classifieds site named Kijiji (since renamed EBayClassifieds.com) to compete with Craigslist. Craigslist claims that the launch of the site was made possible by the release of confidential financial information to eBay’s developers. Among other issues cited in the complaint was a request by eBay’s Pierre Omidyar for information about how Craigslist launched operations in new cities.

Craig Newmark and James Buckminster retaliated by initiating takeover defenses in an effort to seize eBay’s seat on the Craigslist board. eBay sued, and last year a Delaware judge upheld eBay’s rights as a minority shareholder. In 2008, however, Craigslist took its suit to California, countersuing eBay for breach of fiduciary duty and the violation of California’s Securities Law.

The current subpoena issued by the DOJ encompasses information about how eBay was “engaged in alleged criminal activities and misconduct focused around the misappropriation of proprietary/confidential information from Craigslist.” EBay spokeswoman Amanda Miller now says the company “will cooperate with any inquiry related to the disputes between eBay and Craigslist. eBay believes that Craigslist’s allegations against eBay are without merit,” she added.

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