The aim of this study attempts to explore how the structure of the native language and the markedness affect the perception of English vowels by Chinese learners in Taiwan. This paper concerns how people of different English proficiency levels perceive English vowels in terms of the similarity degrees of the vowels in both native and target languages (3 groups × 3 vowel similarity degrees). Thirty Mandarin and Southern Min speaking subjects, equally distributed in three English proficiency levels, namely, low, mid, and high, participated in the study. The quantitative analysis regarded the similarity degrees of the vowels in both native and target languages as three: identical, similar with counterpart, and new. This study also investigated how similar or new vowels are perceived by learners of different English proficiency levels (3 groups × 3 vowel markedness degrees). The similar or new vowels, according to P. Smolensky (1993) and Lombardi (1997), were divided into three categories of markedness: the most marked (rounded and back vowels), marked (front vowels), and unmarked (low vowels). Results showed the influence of both the markedness of English vowels and the different structures between English and native languages. Finally, they were explained via optimality theory.