To understand how specific brain areas associated with transparent motion perception, neural activities during subjects performing a transparent motion perception task were measured by functional MRI (fMRI) and magnetoencephalography (MEG). An integrative fMRI-MEG method, in which the time-varying dipole moments of activated regions were reconstructed from measured MEGs, was applied to data acquired from both fMRI and MEG experiments. Sets of activated regions were determined by statistically analyzing fMRI data and used as spatial constraints for the integrative fMRI-MEG method. Dynamic recurrent neural activities in multiple cortical areas such as V1/V2, left and right intraparietal sulci (IPS) could be successfully detected, suggesting that these three cortical areas play an important role for transparent motion perception. It may also reflect feed-forward and feed-back visual processes among different functional visual areas.