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This study examines online and face-to-face guidance of virtual reality (VR) simulations for understanding a complex topic in genetics. 58 undergraduate students in biology courses that covers the topic participated in the study. 22 learners engaged with the VR simulation with an online facilitator, while 38 learners engaged with a co-located facilitator. We compared the two groups’ understanding of the target topic through pre- and posttests, their mental effort, and sense of presence within the simulation. The co-located group experienced significantly higher posttest scores, while the online group experienced a higher sense of presence in realism. We discuss the implications of our findings for guided inquiry experiences (peer-, teacher-, or tutor-guided) and computing experiences that incorporate configurations with mixed presence.