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Much has been written about the complex textual mechanisms which lie under the structure of academic genre. However, we are still far from a vivid taxonomy of factors that lead to the development of research articles (RAs) as the manifestation of the given genre. Rhetorical structure and thematicity are two of these main parameters. The present study investigates the interaction of the thematic structures and the rhetorical moves of RAs published in the international journals (IJs) and those of the Iranian local journals (ILJs). To this end, a corpus of 120 RA discussion sections of sub-disciplines of Applied Linguistics were analyzed using Kanoksilapatham’s (2007) move analytical model, thematic option (TO) model proposed by Halliday (1985), and the Dane&scaron’ (1974) revised model of thematic progression (TP) in McCabe (1999). The results indicated a significant relationship between the theme types and the generic moves on one hand, and distribution of the theme progressions and rhetorical structures on the other hand. The choice of theme type and thematic progression was found, however, to be, in some cases, influenced by locality of the journals. The findings of the study call for a consideration of a more complex rhetorical profile of RAs than what has to date been assumed.