The employee, who is Head of the Computer Incidents Teams, is under investigation for a period predating his employment at Kaspersky Lab.
Maria Shirokova, Kaspersky's spokeswoman, quoted by the Associated Press, denies that the arrest of Stoyanov has anything to do with the company's operations and that the company has very little details regarding the charges the former manager faces.
The statement added that Kaspersky does not possess any details about the investigation.
It is reported that the arrest is in relation to an investigation into Sergei Mikhailov, who was detained alongside Stoyanov in December 2016. Mikhailov was the deputy head of the Information Security Centre (CDC) of the FSB. One of the sources told Kommersant that investigators verify information on the alleged financial transaction between one of foreign organizations and the Center's employee mediated by employee of one of Russian information security companies. She did admit the fact that the investigation dates back to when Stoyanov was still hired by Kaspersky.
The case is being filed under Article 275 of the Russian criminal code, which is meant to prosecute individuals who take part in "hostile activities to the detriment of the external security of the Russian Federation" and/or provide aid to foreign states or organizations according to Forbes.
Although it was not the first time that Stoyanov deep-dived into how Russian financial cybercrime works, he did write about how Kaspersky hunted for Lurk and helped to catch "one of the most unsafe gangs of financial cybercriminals". "For instance, furnishing the Federal Bureau of Investigation with information on a botnet may amount to treason".
"This case is not related to Kaspersky Lab", the company said.
A much more chilling scenario, offered in this post from Lawfare Blog, is that Stoyanov was a source for U.S. intelligence officers who ultimately concluded Russian-sponsored hacking attempted to interfere with the 2016 USA presidential election.
Russian investigative journalist Andrei Soldatov described the arrest of the Kaspersky manager as "unprecedented".