This study examined how discriminability and prototypicality of nonnative phones modulate the amplitude of the Mismatch Negativity (MMN) event-related brain potential. We hypothesized that if a frequently occurring (standard) stimulus is not prototypical to a listener, a weaker predictive memory trace will be formed and a smaller MMN will be generated for a phonetic deviant, regardless of the discriminability between the standard and deviant stimuli. The MMN amplitudes of Japanese speakers hearing the English vowels /æ/ and /ɑ/ as standard stimuli and /ʌ/ as a deviant stimulus in an oddball paradigm were measured. Although the English /æ/-/ʌ/ contrast was more discriminable than the English /ɑ/-/ʌ/ contrast for Japanese speakers, when Japanese speakers heard the /æ/ standard stimulus (i.e., less prototypical as Japanese /a/) and the /ʌ/ deviant stimulus, their MMN amplitude was smaller than the one elicited when they heard /ɑ/ as a standard stimulus (i.e., more prototypical as Japanese /a/) and /ʌ/ as a deviant stimulus. The prototypicality of the standard stimuli in listeners’ phonological representations modulates the MMN amplitude more robustly than does the discriminability between standard and deviant stimuli.