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Human habitation in deserts can create rich novel resources that may be used by native desert species. However, at night such resources may lose attractiveness when they are in artificially lit areas. For bats, attraction to such manmade habitats might be species specific. In an isolated village in the Negev desert that is known for its high bat activity we investigated the effects of artificial lighting on flight behaviour of two aerial insectivorous bat species: Pipistrellus kuhlii, a non-desert synanthropic bat, common in urban environments and Eptesicus bottae, a desert-dwelling species. Using an acoustic tracking system we reconstructed flight trajectories for bats that flew under artificial lights [Light treatment (L)] versus in natural darkness [Dark treatment (D)]. Under L both P. kuhlii and E. bottae flew significantly faster than under D. Under L, P. kuhlii also flew at significantly lower altitude (i.e. away from a floodlight) than under D. Whereas P. kuhlii foraged both in L and D, E. bottae only foraged in D. In L, activity of E. bottae decreased and it merely transited the illuminated area at commuting rather than foraging speed. Thus, under artificially lighted conditions the non-desert synanthropic species may have a competitive advantage over the native desert species and may outcompete it for aerial insect prey. Controlling light pollution in deserts and keeping important foraging sites unlit may reduce the synanthropic species’ competitive advantage over native desert bats.