Allergic rhinitis and asthma are two prevailing chronic airway diseases and serious public health concerns. Previous research has already described the role of the airway bacteriome in these two diseases, but almost no study so far has explored the mycobiome and its possible association to airway inflammation. Here we sequenced the internal transcribed spacers (ITS) 1 and 2 to characterize the oral mycobiome of 349 Portuguese children and young adults with allergic rhinitis alone (AR) or with asthma (ARAS), asthmatics (AS) and healthy controls (HC). Our genomic analyses showed that the two most abundant fungal phyla (Ascomycota and Basidiomycota) and 3-5 of the 14 most abundant fungal genera in the mouth differed significantly between both rhinitic groups and HC. However, none of the same taxa varied significantly between the three respiratory disease groups (AR, ARAS and AS). The oral mycobiomes of respiratory ill patients showed the highest intra-group diversity, while HC showed the lowest, with all alpha-diversity indices varying significantly between them. Similarly, all disease groups showed significant differences in microbial structure when compared to HC samples. Thirty metabolic pathways were differentially abundant between AR or ARAS and HC patients, but only one of them (D-galactose degradation I) was over abundant in the ARAS group. This study increases our comprehension of the role of the oral mycobiome in allergy-related conditions.