Recently, in several areas of the Middle East, a sharp increase of cutaneous leishmaniasis was observed in suburbs of larger towns including Jerusalem. In some of these areas, poor housing conditions and unsuitable waste management was suspected to provide ideal conditions for sand fly breeding, but hard data on diurnal resting sites and breeding habitats of most sand fly species are scant. In this study, we chose 16 sites on both slopes and the bottom of a natural valley in the Judean Desert to conduct a survey of sand fly distribution with emergence traps. Altogether, 1,261 sand flies, 52% Phlebotomus syriacus, 22% P. sergenti, 14% P. papatasi and 12% P. tobbi were caught. About two thirds of the flies caught were resting, while the other third emerged from breeding sites. All four species showed clear preferences for resting and breeding sites, but generally, most sand flies were breeding in the more humid habitats, namely the bottom of the valley, the adjacent north facing slope, terraces on the north facing slope, and caves. The vegetation cover also appeared to be important for resting habitats; on the bottom of the valley more than six times as many sand flies were collected in areas covered by dense vegetation than in areas with low vegetation cover. P. sergenti seemed also to better tolerate the drier habitats, which might explain the abundance of this species in the arid Judean Desert.