Disclosed are a system and a process for identifying P2P applications and specific P2P software as well from an original mixed packet trace based on behavioral-signatures. The behavioral-signature based system and process according to the invention is mainly to check whether the application has these specific periodic behaviors or not. The process of this invention comprises the steps of filtering out all irrelative packets; translating the filtered packet trace into discrete-time sequences; processing the sequences to obtain frequency-domain characteristics of original packet trace; and analyzing the frequency-domain characteristics and determining the identification.