This paper is to analyze the competitiveness of agricultural exports of Taiwan and Mainland China to Japan and Hong Kong markets. We use market share, export similarity index, relative export performance index and Divisia index to measure the competitiveness. The following results are obtained: (1) The structures of agricultural exports of Taiwan and Mainland China to Japan and Hong Kong are very similar. (2) For Japan market, the products of Taiwan have stronger revealed comparative advantage in the early period, while in later period the products of Mainland China have stronger revealed comparative advantage. The market shares of Taiwan products are generally higher than the market shares of the products of Mainland China, while the expansion of the market shares of Taiwan products is slower. (3) For Hong Kong market, the products of Mainland China have stronger revealed comparative advantage and overwhelming market share.