A court in Moscow said it had ordered that 35-year-old Ilya Sachkov be held in custody for two months, but did not provide further details on the charges.
An unnamed security source told state news agency Tass that Mr Sachkov had denied passing on secret information to foreign intelligence services.
Mr Sachkov has previously been awarded by the Russian president for his work.
His company, Group-IB, specialises in detecting and preventing cyber-attacks and has a global client base that includes the international police agency Interpol.
Group-IB said its offices in Moscow were searched on Tuesday but that it was not clear why. Russia's RIA news agency reported that more searches took place at its St Petersburg offices the following day.
The company said its top management and legal services were "working to clarify the situation".
"Group-IB's team is confident in the innocence of the company's CEO and his business integrity," it said in a statement.
Treason cases in Russia are typically classified, and are punishable by up to 20 years in prison.
Mr Sachkov co-founded Group-IB when he was just 17 and was included on the Forbes magazine "30 under-30" list of tech entrepreneurs in 2016.
At the time, Forbes said he was working alongside banks, Russia's Ministry of Internal Affairs and Europol to help to uncover cyber-criminals.
Three years later, Mr Sachkov was given an award by President Vladimir Putin for his work on identifying and preventing threats to computer systems.
Mr Putin's spokesman Dmitry Peskov said on Wednesday that the Kremlin did not have details about the case.
But Russia's business ombudsman Boris Titov called for answers.
"It is necessary for investigators to explain themselves. Otherwise the sector and its investment attractiveness will be dealt a critical blow," he wrote on Facebook.
Mr Sachkov is the latest in a series of prominent people, including scientists, cyber-security officials, and a former journalist, to be arrested in Russia on treason charges in recent years.
Meanwhile, Moscow has faced numerous allegations of cyber-attacks on Western countries, which it has denied.