Populations of the desert tortoise, Gopherus agassizii, have been severely impacted by upper respiratory tract disease (URTD), a potentially fatal condition caused by Mycoplasma agassizii. Because natural communities of microorganisms in animals may serve as barriers to infection by potential pathogens or may influence the course of a disease, we characterized the bacteria in the nasal passages of captive desert tortoises over an entire season. Tortoises housed in outdoor pens at the Adobe Mountain Wildlife Center in Phoenix, AZ, were divided into four groups: three healthy tortoises that were sampled monthly, three tortoises with signs of URTD that were sampled monthly, three healthy tortoises that were sampled bimonthly, and three healthy tortoises that were sampled once at the end of the season. At each sampling time, the health of each tortoise was assessed and the nares were probed with moistened sterile swabs. The bacteria on the swabs were suspended in sterile saline, serially diluted, and plated on tryptic soy agar medium. Total bacterial counts varied among tortoises from about 10⁴ to 10⁷ per ml and were usually higher in tortoises with signs of URTD. The proportions of different colony types varied from month to month within each tortoise. Although the microbial communities were dominated by pigmented Gram-positive cocci, we also found Gram-positive bacilli, Gram-variable coryneforms, and Gram-negative rods. Many of the same bacteria were recovered from both healthy and URTD tortoises, but others were unique to the URTD tortoises. This study indicates that the nasal passages of desert tortoises contain large continuously changing communities of bacteria and suggests that further analysis of these microorganisms may be useful in assessing the health or stress of populations of desert tortoises and the susceptibility of individual tortoises to URTD.