Because they may demonstrate characteristics of the environment where a body has been laying prior to the discovery, flies are insects of forensic interest. We investigated the fly abundance and the effect of location in Kingdom of Saudi Arabia on fly species diversity that attack decomposing human and animal remains. Using baited traps deployed in each location, we collected 3,697 flies of seven species belonging to three families. Chrysomya albiceps Wiedmann represented 60.86% of the collected flies, whereas Musca domestica L. represented 25.8%; the other species made up < 6% each. To facilitate species identification by DNA barcoding, we sequenced a 710-bp “Folmer region” of cytochrome oxidase subunit 1 (COI) gene for 22 samples from collection sites distributed through entire Saudi Arabia. The COI sequences from Musca albina Wiedmann, Musca lucidula Loew, Musca calleva Walker, Musca sorbens Wiedmann, and Physiphora alceae Preyssler were obtained for the first time. This primary study indicates that even when Folmer primers were widely used in DNA barcoding, the Folmer's region is not adequate when discriminating between Musca species, and sequencing the whole COI or other genes is required for forensic purpose.