The visual P300 brain computer interface (BCI), a popular system for EEG-based BCI, uses the P300 event-related potential to select an icon arranged in a flicker matrix. In earlier studies, we used green/blue luminance and chromatic changes in the P300 BCI system and reported that this luminance and chromatic flicker matrix was associated with better performance and greater subject comfort compared with the conventional white/gray luminance flicker matrix. To highlight areas involved in improved P300-BCI performance, we used simultaneous EEG-fMRI recordings and showed enhanced activities in bilateral and right lateralized parieto-occipital areas. Here, to capture coherent activities of the areas during P300-BCI, we collected whole-head 306-channel MEG data. When comparing functional connectivity between the right and left parieto-occipital channels, significantly greater functional connectivity in the alpha band was observed under the green/blue flicker matrix condition than under the white/gray flicker matrix condition. Current sources were estimated with a narrow-band adaptive spatial filter, and mean imaginary coherence (MIC) was computed in the alpha band. Significantly greater coherence was observed in the right posterior parietal cortex under the green/blue than under the white/gray condition. Reanalysis of previous EEG-based P300-BCI data showed significant correlations between the power of the coherence of the bilateral parieto-occipital cortices and their performance accuracy. These results suggest that coherent activity in the bilateral parieto-occipital cortices plays a significant role in effectively driving the P300-BCI.