In the present STEM (Science, Technology, Engineering, and Mathematics)-driven society, socioscientific issues (SSI) have become a focus globally and SSI research has grown into an important area of study in science education. Since students attending the social and science programs have a different focus in their studies and research has shown that students attending a science program are less familiar with argumentation practice, we make a comparison of the supporting reasons social science and science majors use in arguing different SSI with the goal to provide important information for pedagogical decisions about curriculum and instruction. As an analytical framework, a model termed SEE-SEP covering three aspects (of knowledge, value, and experiences) and six subject areas (of sociology/culture, economy, environment/ecology, science, ethics/morality, and policy) was adopted to analyze students' justifications. A total of 208 upper secondary students (105 social science majors and 103 science majors) from Sweden were invited to justify and expound their arguments on four SSI including global warming, genetically modified organisms (GMO), nuclear power, and consumer consumption. The results showed that the social science majors generated more justifications than the science majors, the aspect of value was used most in students' argumentation regardless of students' discipline background, and justifications from the subject area of science were most often presented in nuclear power and GMO issues. We conclude by arguing that engaging teachers from different subjects to cooperate when teaching argumentation on SSI could be of great value and provide students from both social science and science programs the best possible conditions in which to develop argumentation skills.