With rational water management programs, Saudi Arabia should not be an ideal place for mosquito problems due to its geographical location, weather conditions and, a small amount of exposed water for mosquito population buildup. The aimed to obtain an overview of the biodiversity of Mosquito strains and their bio-control. COI gene-based analyses were used to identify the mosquitoes. The mosquitoes were treated with different concentrations of black seed methanolic extract. About 20 species of mosquito vectors belonging to two genera, based on the morphology one Aedes and one culex was selected for further studies. Aedes and Culex were identified using COI gene sequencing. The partial COI sequence of Aedes aegypti and Culex pipiens was submitted for the accession number. Our results showed remarkable larval activity as well as inhibition of adult emerging percent in the treated groups compared to the control group. This study adds basic knowledge to the molecular evolution of mosquito vectors of medical and veterinary importance and may be useful to improve biotechnological tools employed in the Culicidae control program. Furthermore, this study reveals that black seeds extract can be used for the bio-control of these vectors.