Mosquitoes (Diptera: Culicidae) and biting midges (Diptera: Ceratopogonidae) are among the most important vectors of human and veterinary pathogens. For modelling the distribution of these pathogens, entomological aspects are essential, which in turn are highly dependent on environmental factors, such as temperature. In this study, mosquitoes and biting midges were sampled in multiple microclimates at two low (360, 480 meters above sea level, m.a.s.l.) and two high (1250, 1530 m.a.s.l.) altitude locations in Switzerland. Sets of various traps (CO2‐baited CDC, LED‐UV, resting boxes, oviposition cups) equipped with dataloggers were placed in transects at five sites with similar vegetation at each location. Only the CDC and the LED‐UV traps collected enough insects for analyses. Taxonomic diversity was greater for mosquitoes but lower for biting midges at lower altitudes. Both mosquitoes and biting midges had a thermal preference. Culicoides preferred the traps with warmer microclimate, especially at lower altitudes, whereas mosquito preferences depended on the species, but not on altitude. Relative humidity had a significant positive impact on catches of biting midges but not mosquitoes. To obtain better data on thermal preferences of resting and ovipositing vectors in addition to host seeking individuals, new and improved collecting methods are needed.