Matryoshka RNA viruses (MaRNAV) have been detected using bioinformatics and PCR approaches. They are associated with haemosporidian parasite infections, yet their prevalence and diversity in wild bird populations remain largely unknown. To investigate this, we examined blood samples from wild passerine birds and raptors in the San Francisco Bay Area. Samples were screened for haemosporidian infections followed by RNA sequencing (RNAseq) and reverse transcriptase (RT) PCR to detect MaRNAV. Our analyses identified two novel MaRNAVs (MaRNAV-5 and -6) in various bird species harboring diverse Haemoproteus and Leucocytozoon species. MaRNAV-5, associated with Haemoproteus, exhibited 71.3% amino acid identity to MaRNAV-4 and was found across 15 passerine species. MaRNAV-6, linked to Leucocytozoon, shared 72.9% identity with MaRNAV-3 and was found in 4 raptor species. Prevalence was 44.79% for MaRNAV-5 in infected passerines and 22.22% for MaRNAV-6 in infected raptors. These viruses were not found in uninfected birds and were consistently only in birds infected with haemosporidia. Sanger sequencing revealed high similarity of viral sequences across different bird species. Our findings indicate a high prevalence of MaRNAV among local wild birds, suggesting potential impacts on their health and ecology. We propose a life-cycle model for these viruses where the insect vector is the primary host, and the haemosporidian parasite acts as the virus vector to its next host. Further research is needed to determine the impact of these viruses in avian systems.