The MISEV guidelines of 2018 (DOI: 10.1080/20013078.2018.1535750) are a tremendous resource for extracellular vesicle (EV) research. The guidelines are, however, heavily focused on mammalian EVs, i.e. EVs from humans and laboratory animals chosen for their similarity to humans, where protein cargoes are well characterised, and a wide selection of antibodies are commercially available. Protein markers can be used to identify and define the types of mammalian EV and to determine the presence of any contaminants that might confound functional studies. Similar resources are not as readily available for bacterial EVs as these EVs are not as well characterised, commercially available antibodies are much less abundant and immunological variation between different bacterial species (and there are 1 trillion bacterial species on planet Earth!) means that each species, strain, or group of related species may require different antibodies. To identify quality markers for bacterial EVs, we have characterised the proteome of cells, crude EVs (ultracentrifuge pellet from cell free culture supernatant) and size exclusion chromatography or density gradient centrifugation purified EVs from two different (pathogenic vs probiotic) strains of Escherichia coli grown under two different environmental conditions, and one strain of Mycobacterium marinum grown in one medium. Our results allow the identification of potential markers for EV purity and non-EV contaminants, but also highlight the variability in bacterial EV preparations and suggest potential targets that can be used to investigate the heterogeneity of bacterial EV populations.