•Nonretroviral RNA viruses Endogenous Viral Elements (nrEVEs) are ten folds more abundant in Aedesthan all other mosquitoes.•AedesnrEVEs are enriched in piRNA clusters and produce piRNAs that can limit cognate viral infections.•Few nrEVEs are not in piRNA cluster, encompass complete viral ORFs and are expressed at the mRNA level.•nrEVEs with similarity to Chuviruses are mostly endogenized within Bel/Pao elements and can form a complete retrovirus.•Implementing standardised procedures for nrEVE annotation is necessary to obtain comparable results.