Mosquitoes account for a significant burden of morbidity and mortality globally. Despite evidence of (1) imminent anthropogenic climate and environmental changes, (2) vector-pathogen spatio-temporal dynamics and (3) emerging and re-emerging mosquito borne infections, public knowledge on mosquito bio-ecology remain scant. In particular, knowledge, attitude and practices (KAPs) on mosquitoes are often neglected despite otherwise expensive remedial efforts against consequent infections and other indirect effects associated with disease burden. To gather baseline KAPs that identify gaps for optimising vector-borne disease control, we surveyed communities across endemic and non-endemic malaria sub-districts (Botswana). The study revealed limited knowledge of mosquitoes and their infections uniformly across endemic and non-endemic areas. In addition, a significant proportion of respondents were concerned about mosquito burdens, although their level of personal, indoor and environmental protection practices varied significantly across sub-districts. Given the limited knowledge displayed by the communities, this study facilitates bridging KAP gaps to minimise disease burdens by strengthening public education. Furthermore, it provides a baseline for future studies in mosquito bio-ecology and desirable control practices across differential spheres of the rural–urban lifestyle, with implications for enhanced livelihoods as a consequence of improved public health.