The origin of the felsic volcanic rocks in the Okinawa Trough (OT) remains uncertain. In the middle Okinawa Trough (MOT), two types of rhyolites (type 1 and type 2 rhyolites) have been recognized. Research on the diverse volcanic rocks should be prioritized to determine the magmatic origins of these rocks. Consequently, in this article, the geochemical differences and controlling factors for these two types of MOT rhyolites are systematically discussed. Type 2 rhyolites have higher Dy/Yb and Nb/Ta ratios than type 1 rhyolites, implying that the former might be influenced by a greater contribution of amphibole. Quantitative models suggest that type 1 rhyolites could have formed via the remelting of andesites when amphiboles remain in the source, whereas type 2 rhyolites could have formed without residual amphiboles. These two distinct melting models effectively explain most discrepancies between the major and trace element compositions of type 1 and 2 rhyolites. Additionally, the lower Mg# and δEu values of type 2 rhyolites are partly caused by significant magmatic differentiation. Quasi-linear correlations between some major oxides, trace element ratios and Sr-Nd isotopic ratios for type 2 rhyolites suggest that these rhyolites might have been contaminated by crustal rocks or melts with compositions similar to those of the Kueishantao (KST) andesites or the Middle Miocene upper crustal rocks of SW Japan. Therefore, isotopically enriched crustal materials likely remain in the OT crust.