This article develops a way to conceptualize the complementarity of quantitative and qualitative research in science education. The differing sets of metaphysical presuppositions that give rise to the two approaches are systematically examined by using Stephen Pepper's “world hypotheses”: it is argued and demonstrated that quantitative research is formist/ mechanist in its metaphysical preoccupation, while qualitative research is contextualist/organicist. The vehicle for demonstrating how these metaphysical systems actually influence science education research is Stephen Toulmin's “argument pattern.” It is demonstrated through analysis of examples that quantitative and qualitatitive research reports follow the same pattern of argument, even though the metaphysical roots behind the approaches, which control their differing methodologies and other features, are obviously different. Given the emergence of qualitative research styles, implications are explored for the development of science education research as a total enterprise. Special attention is paid to the problems of appraising the quality of qualitative research reports and to the need for a comprehensive view of what constitutes legitimate research in science education.