This study was undertaken with the goal of developing a Concept Map Knowledge Management System (CMKMS) for use as a tool in observing change in a student's understanding of biology concepts over time. The CMKMS should be useful in assessing the extent of a student's knowledge and in revealing their unique thought processes. The study was concerned not only with a student's self-evaluation of learning but also with their level of satisfaction after using the CMKMS. The CMKMS combines the diagnosis of concept mapping with the style of thought processing, and promotes teaching activities step-by-step, in order to promote effective student learning. In analyzing the factors that influence the effect of teaching, the teacher can determine a student's knowledge structure and highlight misconceptions by inspecting the concept maps and logs. The results of this study show that knowledge management involved in computer-aided instruction in the teaching of biology had a positive influence on learning effectiveness. The CMKMS also was useful in promoting the student's thought processing, creativity, and ability to judge.