Studies have shown that learners need to use self-regulated learning (SRL) skills when learning with Hypermedia Learning Environments (HLEs) to reach a conceptual understanding of science. SRL theory suggests that metacognition plays a key role in learning. The aim of this study was to investigate the relationship between metacognitive monitoring (e.g., judgment of learning [JOL]) and metacognitive control and their effects upon learning about the circulatory system with an HLE. I examined the frequencies of learners' use of negative JOL with and without a change in strategy use, which indicates the quality (i.e., static or adaptive) of metacognitive behavior. The results showed that adaptive metacognitive behavior positively related to learning, and static metacognitive behavior negatively related to learning, above and beyond the effect of prior knowledge. Findings provided valuable implications for the benefits of using JOL followed by control over strategy use when learning with HLEs.