This study investigated how the instruction of argumentation skills could be promoted by using an online argumentation system. This system entitled "Cognitive Apprenticeship Web-based Argumentation" (CAWA) system was based on cognitive apprenticeship model. One hundred eighty-nine fifth grade students took part in this study. A quasi-experimental design was adopted and qualitative and quantitative analyses were used to evaluate the effectiveness of this online system in measuring students' progress in learning argumentation. The results of this study showed that different teaching strategies had effects on students' use of argumentation in the topics of daily life and the concept of "vision." When the CAWA system was employed during the instruction and practice of argumentation on these two topics, the students' argumentation performance improved. Suggestions on how the CAWA system could be used to enhance the instruction of argumentation skills in science education were also discussed.