Strategies applied in this study consisted of a metacognitive strategy combined with cooperative learning (MSCL) and one without cooperative learning (MS). Both strategies used the self-understanding and evaluation sheet (SUES). The aims of this study were to investigate the effect of MSCL and MS on the quality of the learning process in genetics classroom. High- and low-ability students were also compared with regard to the effect of both strategies on their academic performance. Four learning process variables were examined: metacognitive skills, collaborative skills, genetics knowledge, and academic achievement. A quasi-experimental research design was used to compare the MSCL (n = 30) and MS (n = 30) groups in which each group consisted of low (n = 15)-ability and high (n = 15)-ability students. Results showed that MSCL group portrayed higher collaborative skills but lower metacognitive skills than MS group. However, both groups had no influences on other variables: genetics knowledge and academic achievements. In addition, high-ability students performed higher metacognitive skills, genetics knowledge, and academic achievements than low-ability students, whereas both of them showed relatively similar collaborative skills. As a suggestion, this study recommends that metacognitive strategy can be done in collaborative designs by using SUES as the authentic assessment.