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This study explored student perceived shared-metacognition–self-regulation and co-regulation–as explained by three teaching presence sub-elements–instructional design, direct instruction, and facilitation–in an online case-based course. 113 online graduate students enrolled in an advanced instructional design course participated in the study. Data were collected through the Teaching Presence scale of the Community of Inquiry survey and a shared metacognition questionnaire online. The findings revealed Direct Instruction as a significant determinant of students’ shared metacognition. The findings highlight the importance of teaching presence for direct instruction to increase self and co-regulation for maximizing the quality of online case-based course.