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The goal of problem-based learning (PBL) is to help students construct knowledge through engagement in the scientific inquiry process and evaluation of claims. For successful PBL, students need advanced information literacy and argumentation skills to effectively gather, evaluate, and utilize information and data, and then to clarify and justify claims using evidence. The purpose of this study is to design and implement computer-based scaffolds systems to improve high school students’ information literacy and argumentation skills in PBL with a scientific task. The results a) demonstrated the effects of computer-based scaffolding on improving students’ two skills in PBL and b) imply that two skills supported by computer-based scaffolding are pivotal factors in PBL for science learning, which should not be overlooked.