Mental fatigue during long-term motor imagery (MI) may affect intention recognition in MI applications. However, the current research lacks the monitoring of mental fatigue during MI and the definition of robust biomarkers. The present study aims to reveal the effects of mental fatigue on motor imagery recognition at the brain region level and explore biomarkers of mental fatigue. To achieve this, we recruited 10 healthy participants and asked them to complete a long-term motor imagery task involving both right- and left-handed movements. During the experiment, we recorded 32-channel EEG data and carried out a fatigue questionnaire for each participant. As a result, we found that mental fatigue significantly decreased the subjects' motor imagery recognition rate during MI. Additionally the theta power of frontal, central, parietal, and occipital clusters significantly increased after the presence of mental fatigue. Furthermore, the phase synchronization between the central cluster and the frontal and occipital lobes was significantly weakened. To summarize, the theta bands of frontal, central, and parieto-occipital clusters may serve as powerful biomarkers for monitoring mental fatigue during motor imagery. Additionally, changes in functional connectivity between the central cluster and the prefrontal and occipital lobes during motor imagery could be investigated as potential biomarkers.© 2024. The Author(s).