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The COVID-19 pandemic has affected university students globally. Our study investigated mental health indicators among higher degree by research (HDR) students at a regional university in Queensland, Australia. A total of 231 HDR students (female = 137, male = 94) completed the Brunel Mood Scale to assess the constructs of Tension, Depression, Anger, Vigor, Fatigue, and Confusion. A subset of 11 students participated in three focus groups to explore their experiences. Results showed that reported mood among HDR students was generally more negative than population norms, although more positive than moods reported previously during the pandemic. A total of 52 participants (22.5%) reported mood profiles that indicated elevated risk of mental ill-health. Mood profiles varied significantly by gender, age, study mode (full-time/part-time), location (on-campus/online), and citizenship (domestic/international). Quantitative data were supported by focus group findings, which identified mental health and wellbeing as key themes of concern to HDR students. Our findings indicate that support mechanisms to safeguard the mental health and wellbeing of HDR students should be a priority for universities.