Learning model and academic ability are important considerations in developing students' skills including metacognitive skills in biology learning. The study aimed to investigate the effect of open inquiry on the metacognitive skills of students in different academic abilities. The study was quasi-experimental research, using the equivalent post-test only with control group design. The subjects of the experiment comprised 60 eleventh grade students. The samples were randomly assigned in a 2x2 factorial design. Two learning models were compared: open inquiry and conventional models, and two academic abilities: high and low. The students' metacognitive skill was measured by an essay test integrated with academic achievement measurement, as well as an application of a learning journal as self-assessment. The result of a 2-way ANOVA test confirmed the metacognitive skills of students with high and low academic abilities in experiment class was significantly higher than those students in control class, but not for their interactions. Accordingly, the implementation of inquiry-based learning appears to be an effective strategy among students with different academic abilities.