Based on Taiwan's customs statistics, scholars have claimed that the amount of rice exports was greatly reduced in the mid-nineteenth century as Taiwan's main export products changed from rice and sugar in the early Qing to tea, sugar, and camphor after its the ports were opened. However, the customs statistics only include import and export commodities transported via Western ships from four treaty ports (Danshui, Keelung, Anping, and Dagou). By the late Qing, in fact, rice was transported via junks from treaty ports and non-treaty ports alike, so the customs data did not reflect actual rice exports. This article uses shipping and port survey data from the early period of Japanese colonial rule to show that after the Taiwanese ports were opened to Western countries, many of Taiwan's non-treaty ports and shipping concerns (the junk trade) remained prosperous. Their major export was rice. Rice trade statistics from the early Japanese period serve as a basis to re-estimate the amount of rice exports in Taiwan. They indicate that although the rice exports showed a trend of decline in the late Qing, their total value remained the largest amount of Taiwan's exports. Therefore, to discuss the evolution of Taiwan's export market, scholars should give attention to rice exports, non-treaty ports, and the junk trade, all of which were of significance.