Synesthesia provides an elegant model to investigate neural mechanisms underlying individual differences in subjective experience in humans. In grapheme-color synesthesia, written letters induce color sensations, accompanied by activation of color area V4. Competing hypotheses suggest that enhanced V4 activity during synesthesia is either induced by direct bottom-up cross-activation from grapheme processing areas within the fusiform gyrus, or indirectly via higher-order parietal areas. Synesthetes differ in the way synesthetic color is perceived: "projector" synesthetes experience color externally colocalized with a presented grapheme, whereas "associators" report an internally evoked association. Using dynamic causal modeling for fMRI, we show that V4 cross-activation during synesthesia was induced via a bottom-up pathway (within fusiform gyrus) in projector synesthetes, but via a top-down pathway (via parietal lobe) in associators. These findings show how altered coupling within the same network of active regions leads to differences in subjective experience. Our findings reconcile the two most influential cross-activation accounts of synesthesia.