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In Cameroon, <i>Aedes</i> mosquitoes transmit various arboviruses, posing significant health risks. We aimed to characterize the <i>Aedes</i> virome in southwestern Cameroon and identify potential core viruses which might be associated with vector competence. A total of 398 <i>Aedes</i> mosquitoes were collected from four locations (Bafoussam, Buea, Edea, and Yaounde). <i>Aedes albopictus</i> dominated all sites except for Bafoussam, where <i>Aedes africanus</i> prevailed. Metagenomic analyses of the mosquitoes grouped per species into 54 pools revealed notable differences in the eukaryotic viromes between <i>Ae. africanus</i> and <i>Ae. albopictus</i>, with the former exhibiting greater richness and diversity. Thirty-seven eukaryotic virus species from 16 families were identified, including six novel viruses with near complete genome sequences. Seven viruses were further quantified in individual mosquitoes via qRT-PCR. Although none of them could be identified as core viruses, Guangzhou sobemo-like virus and Bafoussam mosquito solemovirus, were highly prevalent regionally in <i>Ae. albopictus</i> and <i>Ae. africanus</i>, respectively. This study highlights the diverse eukaryotic virome of <i>Aedes</i> species in southwestern Cameroon. Despite their shared genus, <i>Aedes</i> species exhibit limited viral sharing, with varying viral abundance and prevalence across locations. <i>Ae. africanus</i>, an understudied vector, harbors a rich and diverse virome, suggesting potential implications for arbovirus vector competence.