Histopathological assessments of young-of-the-year smallmouth bass (YOY SMB) in the Susquehanna River drainage identified a high prevalence of the myxozoan Myxobolus inornatus. This myxozoan infects the connective tissue of the muscle below the skin but is sometimes observed in the esophagus and buccal cavity. In some instances, shallow infections cause breaks in the skin which could increase the chance of opportunistic bacterial infections. Several microbial pathogens including Flavobacterium columnare, Aeromonas spp. and largemouth bass virus (LMBV) have also been cultured from clinically diseased YOY. A multiplex fluorescence in situ hybridization (FISH) assay was developed to determine potential co-localization of M. inornatus, Flavobacterium spp., and Aeromonas spp. infections. With FISH, 75% of YOY SMB exhibited M. inornatus infections, 10% had Aeromonas spp. infections, and 5% had Flavobacterium spp. infections, while 3% had coinfections with both bacterial species and M. inornatus. The results of the multiplex FISH assay revealed a low occurrence of coinfections of Flavobacterium spp. and/or Aeromonas spp. with M. inornatus in randomly sampled individuals.