Akram Azimov, born in 1988, was detained in a village near Moscow, the FSB said in a statement that follows the arrest of his brother — Abror Azimov — on Monday.
The suspected suicide bomber has been named as Akbarjon Djalilov, 22, who is thought to have been a Russian national born in Central Asian Kyrgyzstan.
Abror Azimov, born in 1990, "carried out training of the suicide bomber terrorist Djalilov," the FSB said, calling him "one of the organisers."
At a court appearance, he denied that he helped mastermind the attack, but did admit indirect involvement in it and is being held in custody until June 3 as investigations continue.
His brother Akram "helped transport money used to prepare for the attack, as well as arranging contact with emissaries of international terrorist organisations," the FSB statement said.
No one has claimed responsibility for the attack but investigators are probing possible ties to Islamic State jihadists, who have threatened to attack Russia in revenge for its intervention in Syria.