Our study examined the difficulties Vietnamese Masters (MA) in TESOL (Teaching English to speakers of other languages) students encountered while writing their MA theses. Using a a 5-point Likert scale questionnaire, data were collected from 29 MA TESOL students who had completed their theses at a university in central Vietnam. Fifteen subsequently participated in individual semi-structured interviews. The study found that intense difficulties were voiced around the new genre of writing an MA thesis with its different chapters as subgenres serving different communicative functions. In particular, writing the introduction, the literature review and findings and discussion chapters were the most daunting for the participants. Limited language proficiency was only a surface factor; their top concerns involved how to use appropriate language to express intended meanings, and a lack of awareness about the genre of thesis writing and its communicative functions, alongside plagiarism, critical thinking, and thesis organisation. Cultural influences and a lack of motivation and research experience and perceived self-doubt intensified the perceived difficulties. These findings offer useful implications for key stakeholders in MA TESOL programs in Vietnam and perhaps in similar settings.