In the present study, the nuisance calyptrate species (Order:Diptera) were surveyed during 2010-2011 using sticky traps and nets, at the Empty Quarter Saudi Arabia for identification and genus composition. Samples of flies, a total of 14,400 flies, were collected belonging to six genera from different urban and rural locations at Wadi Eldawser ( Alkhamasin, Elsulayel and Tathleth). Musca domestica was found the most dominant population throughout the year and was abundant indoors all the year being in all sites and represented 58.00 %, of the identified flies. The remaining flies were Musca sorbens (20.40%), Chrysomyia rufifacies (15.1%), Stomoxys calcitrans (5.1%), Sarcophaga species (0.6%), Calliphora species (0.4%) and Fannia species (0.4%). The windy sand storm had a great effect in the depression of the all the flies in-outdoors, however, Musca sorbans was found in a swarm especially after the rain fall. Calliphora, Sarcophaga and Musca fannia were found with higher densities in the rural area of the Sulayel and Tathleth. The obtained results also showed that the highest population densities were observed during March, April, May and June. The depression points in abundance were observed during July and August indicating clear interference with the highest temperature levels. The public health significance of these findings is highlighted.