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Microsoft on Monday named a Russian man as allegedly the guy responsible for running the Kelihos botnet, a spam engine that infected an estimated 40,000 PCs. But closely held data seized from the world’s largest spam affiliate program suggests that the driving force behind Kelihos is a different individual who is still coordinating spam campaigns for hire.

Kelihos shares a great deal of code with the infamous Waledac botnet, a far more pervasive threat that infected hundreds of thousands of computers and pumped out tens of billions of junk emails promoting shady online pharmacies. Despite the broad base of shared code between the two malware families, Microsoft classifies them as fundamentally different threats. The company used clever legal techniques to seize control over and shutter both botnets, sucker punching Waledac in early 2010 and taking out Kelihos last fall.

On Monday, Microsoft filed papers with a Virginia court stating that Kelihos was run by Andrey N. Sabelnikov, a St. Petersburg man who once worked at Russian antivirus and security firm Agnitum. But according to the researcher who shared that intelligence with Microsoft — and confidentially with Krebs On Security weeks prior to Microsoft’s announcement — Sabelnikov is likely only a developer of Kelihos. Rather, the researcher argues, the true coordinator of both Kelihos and Waledac is another Russian man who is well known to anti-spam activists.