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Metadiscourse markers are aspects of a text’s organization denoting a writer’s stance toward its propositional content. Given the ideological difference between quantitative and qualitative research in terms of determinacy, metadiscourse markers can be viewed as a venue through which writers’ epistemological positions are presented. The present study was designed to compare the use frequency of interactive and interactional metadiscourse markers in the discussion section of 20 quantitative and 20 qualitative applied linguistics research articles, with reference to Hyland's (2005) framework. The analysis involved the comparison of frequency counts of metadiscourse markers across the two corpora using a series of Chi-square tests. To that end, the results were computed and analyzed through SPSS. The results revealed significant differences in terms of the frequency of all interactive and interactional metadiscourse markers except for frame markers, evidentials, attitude markers, engagement markers, and boosters. The findings of study have important implications for academic writing instruction.