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This study explored students’ perceptions of their metacognition and its relationships with the CoI framework in an online case-based course. Seventeen online graduate students enrolled in an instructional design course participated in the study. Data were collected through CoI instrument and shared metacognition questionnaire online survey. The findings revealed that co-regulation showed stronger relationships with the three types of online presence than self-regulation. Also, the correlation between two types of metacognition (e.g., self-regulation and co-regulation) was found to be highly. Social presence demonstrated the strongest association with both types of metacognitions, followed by cognitive presence. By contrast, teaching presence revealed the weakest relationship with metacognition. These results suggest that students with higher perceived social presence tend to have higher metacognition.