A longitudinal survey of Anopheles larval habitats was conducted in adjoining areas of Kampung Marabahai, Nangka, Paradason and Tuboh in Kudat District, Sabah from May 2015 to April 2016. Ninety-five out of 368 breeding habitats sampled were positive for Anopheles larvae. The significant physicochemical factors that were associated with the presence of Anopheles larvae were: turbidity, shadiness, presence of water vegetation, surface area, temperature, pH (negative log of the hydrogen ion concentration), and Electrical Conductivity (EC). Thus, this paper highlighted the physicochemical characteristic of larval habitats of Anopheles mosquito with emphasis on An. balabacensis, the vector of Plasmodium knowlesi malaria, could be targeted for surveillance studies and control interventions.