Background: Upper respiratory infections in rabbits (Oryctolagus cuniculus domesticus) present common yet challenging cases for veterinary practitioners. While conventional cultures may only grow a small percentage of microbes, next-generation DNA sequencing (NGS) can be more effective at revealing fastidious or novel organisms. Objective: This study aimed to characterize the rabbit nasal cavity microbiome and determine potential geographical differences. Animals: Clinically healthy pet rabbits from California (CA, n=25) and Alabama (AL, n=24), United States. Methods: Samples were collected via standard protocol of swabbing both nasal cavities. The bacterial and fungal microbiomes were profiled using NGS, targeting the 16S rRNA V1-V3 region for bacteria and ITS-2 for fungi. Results: In total, 186 bacterial taxa were detected, nine representing at least 1% of the microbiome. In each sample, a mean of 37.5 ± standard deviation (SD) of 18 bacterial taxa were detected (mean 36.79 ± SD 19.8 in the AL group, and a mean of 38.20 ± and SD of 17.1 in the CA group). The most abundant bacterial taxa were species within the Pseudomonadales order (mean 12.7% ± SD 17), Moraxella cuniculi (mean 11.9% ± SD 18), and Neisseriaceae sp. (mean 8.5% ± SD 9). Although rabbits were considered healthy, a species within the Mycoplasma genus was detected in 37 out of 49 samples (mean 4.7% ± SD 9). The Helicobacter genus (mean 3.7% ± SD 5.5) and the Campylobacteraceae order (mean 2.84% ± SD 6.1) were also present. The fungal mycobiome was more diverse than the bacteriome, with the most abundant fungal taxa being a species within the Cladosporium genus (mean 38.1% ± SD 25), followed by a species within the Alternaria genus (mean 5.5% ± SD 8), a species within the Pleosporales order (mean 3.8% ± SD 10), Alternaria infectoria-rosae (mean 3.72% ± SD 6.8), Vishniacozyma victoriae (mean 2.93% ± SD 4.4), and a species within the Microascus (Scopularipsis) genus (mean 1.02% ± SD 5.1). Twenty-three fungal taxa were more abundant in the CA group, and three species were more common in the AL group. Clinical Relevance: Findings from this study establish the healthy rabbit nasal cavity microbiome and mycobiome using NGS for veterinary professionals to use a comparison for rabbits with upper respiratory signs.