This empirical study examines how English for Academic Purposes (EAP) university classes in Japan and South Korea approach second language (L2), genre-based writing studies and how students (n=71) perceive their studies in light of recent trends in genre theory pedagogy and methodology. A questionnaire and semi-structured interviews were used to collect data on learner perceptions, while interviews with instructors (n=2) and a review of their teaching materials revealed classroom teaching practices. The results demonstrate that current genre-based teaching methods in Japan and South Korea are not entirely congruent with (a) learners' perceptions of teaching practices that can facilitate academic writing development, (b) genre-based pedagogies in other learning contexts, and (c) what the literature suggests are principles of best practice. The participants call for a more integrated, form- and functionbased approach to genre-based studies. This study argues for more integrated genre pedagogies in Japan and South Korea and provides EAP instructors concerned with best practice a foundation for change regarding genre-based teaching methods. This research also contributes to a better understanding of L2 writing studies in East Asian contexts and advances understandings of learner metacognition as a tool for informing localized L2 writing pedagogies.