The Partenopei have reportedly been tracking the talented midfielder for a number of months and have now made him one of their top summer targets.
Bonaventura's representative, Giocondo Martorelli, has now confirmed that talks are ongoing with Napoli but revealed that it could depend on coach Walter Mazzarri's future at the San Paolo.
"Napoli are tracking Bonaventura, but I also hear talk of a probable change of management," Martorelli told Radio Crc.
"We are waiting to see how the situation evolves. Atalanta are coming off two important wins that have given them real confidence."
Bonaventura came through Atalanta's youth academy and has now made 89 Serie A appearances for the side, scoring 17 goals.