The numbers of potentially pathogenic microorganisms that have been isolated from stranded cetaceans in the last three decades underscore the urgent need for methods of detection of microorganisms that might cause significant disease and increase the likelihood of population declines. We have designed and implemented two non-invasive techniques for the collection of exhaled breath condensate (blow) from free-ranging whales and demonstrated their suitability for the detection of respiratory bacteria. We successfully collected 22 individual blow samples from eight cetacean species. Using well-established molecular techniques we detected three bacterial genera (Haemophilus, Streptococcus and Staphylococcus). Haemophilus spp. was detected in fin whale Balaenoptera physalus, sperm whale Physeter macrocephalus, humpback whale Megaptera novaeangliae and gray whale Eschrichtius robustus blows, while unidentified β-hemolytic streptococci and Staphylococcus aureus were detected in gray whale and blue whale Balaenoptera musculus blows. The detection limit of the test was determined as 1 CFU mL−1. None of the identified bacteria were found in environmental (control) samples, suggesting that their presence in the blows was genuine and not due to inadvertent contamination. While the population-level relevance of these bacteria is as yet unclear and it is possible that they are commensal microorganisms, S. aureus has been identified previously as a high-risk pathogen to cetacean health, and streptococci have increasingly been associated with cetacean mortality events. We suggest that future cetacean monitoring programs of vulnerable or threatened species include blow sampling as a means to determine the prevalence of the respiratory bacteria in the populations and monitor spatiotemporal fluctuations as indicators of changes in cetacean health.