Methods and apparatus to identify media application sessions are disclosed. An example apparatus includes an audio interface to monitor an audio output of a media presentation device during a viewing session, a tone analyzer to identify one or more dual-tone multi-frequency (DTMF) tones presented by the audio output of the media presentation device, a session identification determiner to determine a session identification value associated with the viewing session based on the one or more identified DTMF tones, and a session report generator to associate a panelist identifier with the viewing session, and generate a session report based on the session identification value associated with the DTMF tones and the panelist identifier associated with the viewing session.