Background: The primary objective of this paper is to provide a review of research on argumentation in science education based on publications from 1998 to 2014 in three science education journals. In recent years, the teaching and learning argumentation (i.e. the coordination of evidence and theory to support or refute an explanatory conclusion, model or prediction) has emerged as a significant educational goal. Argumentation is a critically important discourse process in science and it should be taught and learned in the science classroom as part of scientific inquiry and literacy. Argumentation stresses the evidence-based justification of knowledge claims, and it underpins reasoning across STEM domains. Our aim in this study was to investigate how argumentation has been positioned within the publications of three top academic journals: "Science Education," "International Journal of Science Education," and "Journal of Research in Science Teaching." A methodology for content analysis of the journals is described using quantitative and qualitative techniques. Results: One of the contributions of our analysis is the illustration that researchers studying argumentation from a linguistic perspective have been emphasizing related concepts in different ways. While the emphasis has been on discourse and discussion across all journals, the related concepts of talk, conversation, dialogue and negotiation were observed to a lesser extent. Likewise, the fine-level analysis of the key epistemic concepts such as reasoning, evidence and inquiry indicates variation in coverage. Conclusions: The findings can provide evidence-based indicators for where more emphasis needs to be placed in future research on argumentation, and in particular they can provide guidelines for journals in soliciting articles that target underemphasized aspects of argumentation in science education.