This study aimed to highlight the low host specificity of Hippobosca equina (H. equina) that poses a danger in diseases transmission between different animal species as well as, identification of the collected flies using light microscope and molecular characterization of H. equina in Egypt. Two hundred and forty flies were collected weekly from different animal species from El-Faiyum, Al Qalyubia and Kafr El-Sheikh Governorates, Egypt at the period from May to September of 2020. Insects were phenotypically and genetically identified then classified into 170 (70.8%) males and 70 (29.2%) females. The highest prevalence of H. equina was noticed from mid-June to the end of August. The sequencing of COI gene of five H. equina fly collected from different hosts as (horse, pigeon, cattle, buffalo, and donkey) were submitted to the GenBank under the accession numbers of MZ452239, MZ452240, MZ461943, MZ461944, and MZ461945, respectively. For insect infestation control, fipronil and deltamethrin is monthly sprayed for animals, birds and their circumference give a best result in our control study in the field. Deltamethrin showed a success in the elimination process and control measures of external parasites of pigeon.