The aim of this study is to contribute to cross-cultural and cross-disciplinary discourse analysis, shedding light on English L2 learners’ metadiscursive practices. Focusing on a specialised learner corpus of English-medium Master’s theses written by Czech university students, the research explores the occurrence of endophoric markers and their characteristics. To enable cross-linguistic and cross-cultural comparison, a reference corpus of representative L1 English academic discourse was compiled. A new taxonomy used here, which draws on Hyland’s list of endophoric markers (2005) and an extensive literature review, categorises endophoric markers into three groups: purely directional, markers using specific words, and a category combining the first two. The study investigates the occurrence and function of these markers, focusing on anaphoric, cataphoric, and non-directional references. It also aims to identify differences in the usage of endophoric markers in English between L2 novice writers and experienced L1 academic writers, providing insights into trends and patterns in the employment of endophoric markers in academic writing in a way that accounts for disciplinary and linguistic factors. The results reveal higher endophoric marker frequencies in the Master’s Thesis Corpus, suggesting distinctive discourse patterns among Czech learners using English as an L2, with a predominance of specific endophoric markers and notable cross-disciplinary variation.