Purpose Vernal keratoconjunctivitis (VKC) is a severe form of ocular allergic disease possibly related to an altered ocular surface microbiota. The aim of the study was to determine the bacterial and fungal composition of conjunctival microbiota in VKC compared with healthy controls (HC). Methods Lower fornix conjunctival swabs were obtained from 22 VKC children and 20 age, sex and ethnicity-matched HC. Total DNA was extracted, and used for 16S rRNA and ITS2 gene amplification and sequencing. Results High-throughput sequencing of 16S rRNA and ITS2 amplicon libraries produced a total of 734,157 and 677,115 high-quality reads, respectively. Clustering of similar sequences (>97% of identity) resulted in 1,241 and 933 OTUs, respectively. Alfa and beta diversity metrics highlighted significant differences of conjunctival bacterial and fungal microbiota composition in VKC patients and HC. Proteobacteria, Firmicutes and Actinobacteria phyla were present in all subjects qualifying theme as a putative core microbiome of both HC and VKC groups. In addition, Bacteroidetes and Fusobacteria met the core microbiome’s definition criteria in VKC patients. Of the 132 observed families, Moraxellaceae showed a higher abundance in VKC group than HC. Saccharomycetaceae, Malasseziaceae, and Dipodascaceae were present in all subjects, constituting the fungal core microbiome of both HC and VKC patients. OTUs referred to Malasseziaceae were significantly higher in VKC children compared to HC. Conclusion VKC patients and healthy controls have different conjunctival microbiomes. These results may provide new insights into the complex VKC pathogenesis.