Developing student's critical thinking skills (CTS) has become an important issue in higher education. This study developed an effective assessment method, focusing on qualitatively evaluating student's CTS demonstrated through asynchronous online discussions. Examples of how the online discussions were coded and analyzed based on the developed coding scheme will be demonstrated. The developed qualitative assessment provides a valuable tool for researchers and educators to foster, monitor and analyze students' CTS more objectively and systematically in computer conferencing applications. In addition, the research results also indicated that with appropriate course design and instructional interventions, CTS can be fostered in asynchronous online discussions.