Research on motor sequence acquisition has shown significant differences between learners. Learners who develop explicit knowledge respond faster than non-explicit ones and they show larger amplitude in event-related brain potentials to sequence deviants. There is evidence that memory span correlates with the amount of sequence learned, but the specific mechanisms subserving such differences are still unknown. Recently, it has been observed that performance of explicit learners, but not of non-explicit ones, improves when presented with auditory action effects. Accordingly, differences between learners might be related to differences in auditory rhythm perception. To test this hypothesis, the mismatch negativity (MMN)-evoked potential elicited to stimuli violating stimulus alternation (i.e. low pitch, high pitch) was recorded in explicit and non-explicit sequence learners. Results confirmed our prediction: explicit learners showed larger amplitude of the MMN to the violation of the auditory rhythm, suggesting new theoretical implications to account for individual differences in sequential action control.