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Background: Malaria remains one of the most prevalent and fatal diseases among the inhabitants of Palawan in the Philippines. Palawan, where healthcare services remain limited, has the highest malaria endemicity in the country. To eliminate malaria, effective prevention measures should be conducted alongside early diagnosis and prompt treatment, which are the major tasks of the trained microscopists in Palawan. However, while the microscopists have implemented community awareness-raising activities aimed at preventing transmission of malaria, the nature and quality of these activities have not been evaluated. The present study identified the factors associated with the strengthening of community awareness-raising activities for malaria prevention implemented by microscopists in Palawan. Methods: A cross-sectional study was conducted among 127 microscopists in Palawan. Data were collected using self-administered questionnaires from November 2010 to February 2011. For data analysis, structural equation modelling was conducted, based on the questionnaire results, to identify the impact of factors associated with the number of community malaria awareness-raising activities implemented by microscopists using the following assessment indicators: (1) place of assignment; (2) annual parasite index; (3) microscopists’ capacity (service quality, knowledge on malaria, and ability in malaria microscopy); (4) self-preventive measures against malaria; and (5) job satisfaction. Results: High microscopists’ capacity was found to be a significant factor for a greater number of community awareness-raising activities for malaria prevention. High microscopists’ capacity was significantly explained by its two sub-components: high service quality (active detection, diagnosis and treatment, prescription of anti-malarial, and follow-up) and high ability in malaria microscopy (preparation and documentation, slide preparation and observation, safe handling and disposal, and knowledge on the morphology of infected red blood cells). Conclusions: Microscopists’ capacity was identified as a significant factor in community awareness-raising activities for malaria prevention. Thus, the strengthening of service quality and ability in malaria microscopy should be of the highest priority.