AbstractBackgroundHispanic people with cystic fibrosis (CF) have decreased life expectancy and earlier acquisition of Pseudomonas aeruginosa compared to non‐Hispanic white individuals with CF. Racial and ethnic differences in the airway microbiome of CF may contribute to known health disparity, but have not been studied. The objective was to describe differences in the upper airway microbial community in Hispanic and non‐Hispanic white children with CF.MethodsThis prospective, observational cohort study of 59 Hispanic and non‐Hispanic white children with CF, ages 2−10 years old, was performed at Texas Children's Hospital (TCH) from February 2019 to January 2020. Oropharyngeal swabs were collected from the cohort during clinic visit. Swab samples underwent sequencing (16S V4 rRNA), diversity analysis, and taxonomic profiling. Key demographic and clinical data were collected from the electronic medical record and the CF Foundation Patient Registry (CFFPR). Statistical analysis compared sequencing, demographic, and clinical data.ResultsWe found no significant difference in Shannon diversity or relative abundance of bacterial phyla between Hispanic and non‐Hispanic children with CF. However, a low abundant taxa‐ “uncultured bacterium” belonging to the order Saccharimonadales was significantly higher in Hispanic children (mean relative abundance = 0.13%) compared to the non‐Hispanic children (0.03%). Hispanic children had increased incidence of P. aeruginosa (p = 0.045) compared to non‐Hispanic children.ConclusionWe did not find a significant difference in the airway microbial diversity between Hispanic and non‐Hispanic white children with CF. However, we found a greater relative abundance of Saccharimonadales and higher incidence of P. aeruginosa in Hispanic children with CF.