The study investigated the effect of graphic organizers on students' levels of conceptual understanding, and the effect of students' cognitive level on conceptual understanding. The control group (n=40) received a conventional classroom instruction while the experimental group (n=38) received an innovative classroom instruction, using graphic organizers. A mixed-method research design was employed. Pre-test, post-test, and Lawson's Classroom Test of Scientific Reasoning were utilized to compare quantitative results within and between groups. Qualitative data were gathered using structured interview schedule to further corroborate the quantitative findings. In comparison, results show that the experimental group significantly outperformed control group based on post-test results: remembering (p=0.001), analysis (p=0.001) and thinking beyond (p=0.013), except for application (p=0.906) which is not statistically significant. Furthermore, the correlation results show that, overall, there are no strong and significant correlations between students' concrete operational and transitional cognitive levels, and levels of conceptual understanding in both pre-test and post-test results for control and experimental groups. Since students' cognitive levels have no significant effect in enhancing students' conceptual understanding, therefore, the outperformance of the experimental group was due to the use of graphic organizers integrated in lesson packages.