Stance in general and metadiscourse markers, in particular, have attracted the interest of several studies. Therefore, this study explores the use of metadiscourse in the second language (L2) academic writing by English as a foreign language (EFL) postgraduates in one of the Malaysian public universities. We analyzed the frequency and wordings of modality within the citations of the literature review chapters of 20 Ph.D. theses employing the Systemic Functional Linguistics. Data were analyzed manually utilizing the technique of quantifying the findings to highlight the similarities and differences in using metadiscourse markers. The findings revealed the dominance of full declarative clauses in both Applied Linguistics and Information Technology. Besides the Finite Modal Operators, Mood Adjuncts and Comment Adjuncts were also used to demonstrate modality with a variety in their stance, degrees, and frequencies. Pedagogically, these findings could help supervisors in identifying the implications of their students’ writings. In addition, students can be directed towards reading EAP textbooks and materials that are dedicated to areas of academic writing, metadiscourse markers, and citations.