Giovanni Di Napoli, 60, was arrested on Monday over the triple murder in Italy’s southern Puglia region, Ansa reported.
He is thought to have orchestrated the drive-by shooting on March 17th 2014, in the Palagiano area, in which toddler Domenico was killed.
The boy’s mother Carla Fornari was also murdered, along with her partner Mimmo Orlando.
The woman’s two other children, aged six and eight, reportedly survived by playing dead. The children’s biological father was murdered in 2011, Ansa said.
Di Napoli, who has in the past been convicted for mafia association and murder, is accused of ordered the family’s slaying to settle a personal dispute with Orlando.
When he was killed Orlando was being accompanied by Fornari back to prison, under the terms of a custodial sentence.
The killings shocked Italy and led to renewed debate over the mafia’s so-called “code of honour”, described as a myth in the wake of the toddler’s murder.
The Puglia killings came just two months after another toddler was killed by the mafia in the Calabria region. The charred skeleton of Nicolino Campolongo was found in a burnt-out car along with the bodies of his grandfather, a convicted drug trafficker, and the man’s partner.
A 50 cent coin was left on the car bonnet, thought to be a symbolic move to show the value the killer put on their victims’ lives.