In the current study, bacteria were identified in zebra mussel samples collected from the Huron River, Crystal Lake, and Vineyard Lake, Michigan. Bacteria were identified by sequencing the 16S ribosomal RNA gene of amplified community bacterial DNA extracted from mussel homogenate samples. More than 170 zebra mussel bacterial 16S gene sequences were checked for similarity to 16S sequences contained in the Ribosomal Database Project and BLAST public databases. Analysis demonstrated the presence of 27 bacterial genera belonging to 12 subdivisions in tissues of zebra mussels collected from the 3 locations. Potentially pathogenic bacteria for aquatic and terrestrial animals, like Aeromonas spp., Flavobacterium spp., Pseudomonas fluorescens, Shewanella putrefaciens, and Shigella sp. were also detected in mussel homogenates raising concerns that this invading mussel may play a role in disease ecology. Data generated in this pilot study constitute the first account of bacterial community composition in the zebra mussel in Michigan waters and underscore the need to understand better the bacteria-host relationship in invading dreissenids in their new environment in the Laurentian Great Lakes.