Abror Azimov, who was born in 1990 and is reported to be from Kyrgyzstan, had "fully confessed" to organising the blasts, his lawyer told Russian media.
He is the ninth person to be detained in connection with the 3 April attack, which was carried out by Kyrgyz-born Russian Akbarzhon Jalilov, 22.
The blast left over 50 people injured.
Russian security services previously said they believed Abror Azimov "carried out training of the suicide bomber terrorist Jalilov".
The other eight people detained in connection with the attack - six in St Petersburg and two in Moscow - are also from Central Asia.