Mosquitoes are vectors of viruses affecting animal and human health. In Iran, the prevalence of mosquito-borne viruses remains poorly investigated. Once infected, mosquito females are infected for all their life making virus detections possible at early steps before infections are reported in vertebrate hosts. In this study, we used a recently developed high-throughput chip based on the BioMark Dynamic arrays system capable of detecting more than 50 arboviruses in a single experiment. A total of 1,212 mosquitoes collected in Mazan-daran, North-Khorasan, and Fars provinces of Iran were analyzed. Eighteen species were identified, belonging to five genera; the most prevalent species were Anopheles maculipen-nis s.l. (42.41%), Culex pipiens (19.39%), An. superpictus (11.72%), and Cx. tritaenior-hynchus (10.64%). We detected chikungunya virus (CHIKV) of the Asian genotype in six mosquito pools collected in North Khorasan and Mazandaran provinces. To our knowledge, this is the first report of mosquitoes infected with CHIKV in Iran. Our high-throughput screening method can be proposed as a novel epidemiological surveillance tool to identify circulating arboviruses and to support preparedness to an epidemic in animals and humans. Author summary Mosquito-borne viruses pose a serious threat to public health worldwide. For an efficient preparedness to future emergences, an early detection of arboviruses in vector populations would be wise before animal/human cases arise. Here, we used a recently developed high-throughput chip based on the BioMark Dynamic arrays system, capable of screening various arboviruses in a single experiment. By examining 1,212 mosquitoes collected in Iran, we provide evidence that chikungunya virus was circulating in Iran. PLOS NEGLECTED TROPICAL DISEASES PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.