Acquiring literacy establishes connections between the spoken and written system and modifies the functioning of the spoken system. As most evidence comes from on-line speech recognition tasks, it is still a matter of debate when and how these two systems interact in metaphonological tasks. The present event-related potentials study investigated the role and activation time course of the phonological and orthographic representations in an auditory same/different phoneme judgment task in which the congruency between phoneme and grapheme was orthogonally manipulated. We reported distinct time windows and topographies for phonological and orthographic effects. The phonological effect emerged early at central and parietal electrode sites and faded away later on, whereas the orthographic effect increased progressively, first observable at central and parietal sites before generalizing at the frontal site. These effects are clearly different from what has been reported in speech recognition tasks and suggest that our cognitive system is flexible enough to adjust its functioning to respond to the task demands in an optimal way. (Contains 1 table and 1 figure.)