This paper examines how Europeans depicted Taiwanese waters in maps and charts in the sixteenth century and early seventeenth century. Those maps and charts constitute important record of European knowledge about East Asia in the sixteenth century. In this paper, the author focuses on two toponyms: "Lequeo Pequeno" and "Formosa", explaining the origins and usage of the two terms. By analyzing the toponyms and the respective drawing styles, we can categorize these European maps and charts into four groups: Mercator type, Homem type, Ortelius type, and Dourado type. While these charts reflected contemporary ideas and new discoveries of the sixteenth century, European perceptions of Taiwanese waters, e.g., the location of "Lequeo Pequeno" and "Formosa", were obscure and confused. The diversity of European "local knowledge" and charts didn't change until the Dutch East India Company (VOC) entered Taiwanese waters in 1620s. They then conducted a survey and mapped of Taiwanese waters, in the process of which the VOC only discovered one big island which they named "Formosa" or "Pacan". Such a discovery turned out to be a striking advance in European map-making. Furthermore, it signaled the end of Portuguese marine activities, with the VOC emerging as the new force to define seventeenth-century geography of the waters surrounding Taiwan, and East Asia in general.