Asthma affects millions of children worldwide and has been associated with alterations in airway microbiota. This study used 16S rRNA sequencing to characterize the nasal and oral microbiota of 63 asthmatic and 89 healthy children from Santiago, Chile. Results showed significantly lower alpha diversity and over-abundance of pathogenic genera in nasal samples from asthmatics compared to healthy subjects. Community structure analysis revealed different microbial interactions in asthmatic and healthy subjects, particularly in the nasal microbiota. Detection of 51 functional pathways differentially abundant in the nasal mucosa of asthmatic subjects identifies potential taxonomic and functional biomarkers of pediatric asthma.