Wolbachia suppresses the replication of +ssRNA viruses such as dengue and Zika viruses in Aedes aegypti mosquitoes. However, the range of viruses affected by this endosymbiont is yet to be explored. Recently, novel insect-specific viruses (ISVs) have been described from numerous mosquito species and mosquito-derived cell lines. Cell-fusing agent virus (Flaviviridae) and Phasi Charoen-like virus (Bunyaviridae) persistently infect the Ae. aegypti cell line Aag2 which has been used for experimental studies with both the wMel and wMelPop-CLA strains. Wolbachia was found to restrict the replication of CFAV but not the PCLV infection in these lines. Furthermore, an additional Ae. albopictus cell line (RML-12) which contained either wMel or wMelPop-CLA was assessed. While no infectious +ssRNA or dsRNA viruses were detected, a PCLV infection was identified. These observations provide additional evidence to support that insect-specific, +ssRNA viruses can be suppressed in cell culture by Wolbachia but -ssRNA viruses may not.