We conducted a multiple cross-over experiment from April 2013 – April 2014, in which all houses in one of two villages in Mondolkiri Province, Cambodia were alternately supplied with an emanator of the spatial repellent metofluthrin per 30 m3 of protected area to cover all potential peridomestic areas where people might spend their time before sleeping. Emanators were replaced every month for a three-month period. Mosquito densities were simultaneously monitored in each village for two weeks every month using six CDC light-traps/night run from 18.00 to 07.00 hrs inside bedrooms and malaria prevalence, seroconversion and gSG6 protein rates assessed from prevalence surveys. After emanators were installed in the first village they were installed in the second village for a further three-month period and following that were again used in the initial village for a further three months. Surveys were undertaken before the initial installation of the emanators and at each cross-over point. Anopheles dirus densities were highest in houses closest to the forest. Transmission rates were low even before the application of the emanators. Perhaps due to the low levels of malaria transmission in Mondolkiri no significant relationships were found in Plasmodium cases or seroconversion rates between villages, surveys or by intervention. Adult males, who might spend more time unprotected in the forest at night, appeared to be at greater risk of becoming infected with P. falciparum malaria as compared to women or young children. At the malaria transmission levels present in Mondolkiri the metofluthrin emanators evaluated had no observable effect on malaria prevalence. This may be due to confounding by low prevalence rates.