Employing Halliday’s (1994) Systemic Functional Grammar approach, the present study examines the Korean EFL college students’ way of organizing thematic structures in written English texts, with special focus on the influence of learner proficiency. A total of 150 learners’ argumentative essays consisting of 50 essays each from three levels of learner groups were compared with 50 essays from its native counterparts, with inquiry focused on the thematic selection, usage of various theme features, and semantic distribution of topical themes. The results show that textual themes, multiple themes, and first person pronouns as topical themes are highly overused in the learner texts compared to the native essays. Overall, the level of proficiency significantly affects learners’ choices regarding thematic structures although the enhanced proficiency does not involve the improvement in all aspects of thematic organization. From these findings, it is suggested that the EFL writing pedagogy should pay greater attention to the effective use of thematic organization as a means of enhancing textual coherence and embrace level-specific instructions.