Abstract: Plant microbial communities (microbiota) living on the surface of fruit have been the source of the majority of biocontrol agents (BCAs), but their role as a community has been poorly studied so far. A pioneering assay using high-throughput sequencing (HTS) has been carried out to get insight into the microbiota of apple (cv. Pinova) surface through metagenome sequencing. Fruit of cv. Pinova was sampled in Belgium during autumn 2013, and then the microbiota was isolated. After DNA extraction, the HTS assay generated 14.5 Gbases, which were assembled in 133.888 contigs. These contigs provided useful information on taxonomic composition of the microbiota. A total of 1863 bacterial species and 1194 fungal species have been identified. Our results demonstrated a very diverse microbial community on conventionally treated apple cv. Pinova, and its role needs to be characterized.