Metatranscriptome sequencing has emerged as a powerful tool for uncovering viral diversity in insects and their associated microbes. To explore viruses linked to the pea aphid (Acyrthosiphon pisum), we performed metatranscriptome sequencing on field-collected samples. In addition to several known plant viruses, we assembled the genome of a new virus homologous to species in the family Mitoviridae, which are positive-sense single-stranded RNA viruses that encode only an RNA-dependent RNA polymerase and typically replicate in mitochondria. Given the frequent association of mitoviruses with fungi and the presence of entomopathogenic fungal reads in our dataset, we conducted 18S amplicon sequencing and PCR screening on individual aphids. These analyses identified two fungal entomopathogens and uncovered an association between the mitovirus and Zoophthora radicans, a generalist aphid pathogen. Our findings shed light on the hidden microbial diversity in natural pea aphid populations and emphasize the utility of metatranscriptomics in identifying novel virus-host associations.