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This study investigated high school students' perception and understanding of scientific argumentation. The sample consisted of 245 high school students. Two questionnaires were administered with the sample resulting in quantitative data. Qualitative analyses of students' responses were also carried out. The results indicate that students' understanding of scientific argument particularly with respect to their differentiation of justification is quite limited. Students have difficulties in understanding types of justification. Even though students appreciate the role of argumentation and discourse in science teaching and learning, their perceptions of the use of various strategies in the implementation of argumentation were contradictory. Students' perceptions of discourse are based on categories classified as knowledge, implementation, understanding, importance of science, actions by students and teachers, and classroom management. Students' perceptions' of argumentation include similar themes as in perceptions of discourse. There were only two different themes which were related to knowledge and nature of science instead of classroom environment and importance of science, respectively. This study contributes to the evidence base for understanding the connection between students' argumentation perceptions and their improved engagement in argumentative discourse. Additionally, the study suggests the need for developing students' metacognitive skills.