Airway microbial metagenomes are studied with increasing frequency in the context of acute or chronic lung diseases. Data on the microbial community composition in the airways of healthy people, however, is rather scarce. The Human Microbiome Project (HMP) did not contribute such data either. While microbial communities from various other sites in healthy human hosts were analysed by metagenome sequencing in this project, lung parenchyma and tracheobronchial tracts were not included as target sites, since they were still considered as sterile at that time. Research efforts have proven the presence of microbial communities also in these parts the airways of healthy people recently, and data on community composition has been collected, mainly based on 16S rRNA gene sequencing. Especially data based on full metagenome sequencing, which allows better discrimination on the species level and even analysis of species co-occurrence networks, however, is barely available. Therefore, we set up a study in which airway samples were collected from healthy people with no history of pulmonary diseases Donor were between 10 and 60 years of age, and either sputum or throat swab samples were collected. After DNA extraction, full metagenome sequencing was applied to 156 sputum and 172 throat swab samples in total. The resulting data was used for studying microbial community composition, similarity and/or diversity, network analyses and associations with age. The datasets can also be used for comparative studies with airway metagenome data from samples with disease background.