We have identified the brain areas involved in Manual Preference (MP) in 143 left-handers (LH) and 144 right-handers (RH). First, we selected the pairs of homotopic regions of interest (hROIs) of the AICHA atlas with significant contralateral activation and asymmetry during the right hand and the left hand Finger-Tapping (FT) both in RH and LH. Thirteen hROIs were selected, including the primary and secondary sensorimotor and premotor cortices, thalamus, dorsal putamen, and cerebellar lobule IV. In both groups, contralateral activations and ipsilateral deactivations were seen, with stronger asymmetries when the preferred hand was used. Comparing with different models for the prediction of MP, we found that the differences in activity during preferred hand minus non-preferred hand movement in 11 contralateral and/or ipsilateral hROIS were best at explaining handedness distribution. Two different mechanisms were identified: 1. Stronger contralateral activity of cortical and cerebellar motor areas during right hand movement, seen in both groups but modulated by handedness; 2. Stronger deactivation in ipsilateral areas during dominant hand movement in both groups, LH here mirroring RH. The present study thus demonstrates that handedness neural support is complex and not simply based on a mirrored organization of hand motor areas.