The first part of this chapter (Sections 2.1–2.4) will introduce the theoretical background to written discourse analysis with a special focus on cohesion and genre analysis to show the place of reference from a wider perspective. The central concepts used in this book are defined in Section 2.2. Section 2.3 will give a brief outline of approaches in written discourse analysis including cohesion analysis and methods of discourse analysis, providing a quick overview of influential taxonomies and research since the 1970s. Given that cohesion has been demonstrated to be significantly influenced by genre and text type, and because the purpose of this study is to compare two distinct genres, Section 2.4 will be devoted to genre analysis. First, the concept of ‘genre’ will be defined, and then a method for analyzing genres as applied in this study will be discussed. The most important findings about teaching and learning English for Academic Purposes (EAP) are summarized in Section 2.4, with a focus on the challenges faced by non-native students learning to use EAP. Section 2.5 of the review of the literature will focus on the two genres (or rather, subgenres) this study intends to compare: RAs and MA theses. The motivation for comparing these two subgenres will be justified by describing their textual and generic features, and highlighting the expected pedagogical implications that the comparison intends to reveal. It will also show how reference as a cohesive device is problematic for non-native speakers of English (NNSs), thereby providing the rationale and context for this study in written discourse analysis.