The practices of argumentation have recently been upheld as an important need to develop students' understanding of scientific concepts. However, the present education system in Malaysia is still largely examination-based and teacher-oriented. Thus, this study aims to examine the mastery level of scientific argumentation and its scheme among Malaysian secondary-level science students. A total of 120 students were randomly assigned to answer a Scientific Argumentation Test (SAT), either individually or in a group. Based on the answers, two groups of students, one who have answered with valid scientific concepts and another who have answered with invalid concepts, were identified and interviewed. Quantitative analysis was performed on the SAT results to determine students' mastery of scientific argumentation, and their argumentation schemes were assessed using content analysis performed on the interview transcripts. The results showed that students were weak in the construction of scientific arguments with valid concepts. Moreover, most of the constructed arguments consisted of misconceptions. The results also showed that students who were involved in group argumentation tended to have a more complex argumentation scheme, compared to individual students. As a group, students were able to argue with more scientific elements and showed their understanding of macro and submicro concepts. Hence, science teachers need to emphasize on the construction of scientific argumentation in their teaching, especially at the macro, submicro, and symbolic levels of representations, to ensure students' understanding of the concepts. This will therefore enhance their mastery of scientific argumentation and improve their content knowledge.