This study examined the effect of online metacognitive strategies, hypermedia annotations, and motivation on reading comprehension in a Taiwanese hypertext environment. A path analysis model was proposed based on the assumption that if English as a foreign language learners frequently use online metacognitive strategies and hypermedia annotations, then they would increase their learning motivation, which, in turn, would enhance their hypertext comprehension performance. Participants consisted of 37 English majors enrolled at a private university in southern Taiwan. The results revealed that online metacognitive strategies most significantly predicted learning motivation and motivation directly affected hypertext comprehension. However, metacognitive strategies and hypermedia annotations did not directly affect hypertext comprehension. Consistent with expectations, motivation was found to mediate the relation between online metacognitive strategies and hypertext comprehension. On the other hand, the relation between hypermedia annotations and hypertext comprehension mediated by motivation was not obvious. Finally, the implications of these findings for future research are discussed and presented.