Illumina Next Generation Sequencing (NGS) platform targeting the conserved regions of bacteria ribosomal DNA (16s rRNA) was used to identify the bacterial community associated with soursop (Annona muricata L.). The aim of this work is to compare the diversities of the bacterial communities of Annona muricata and Malus domestica (obtained from National Centre for Biotechnology Information (NCBI) database). The functional genes in these communities were also predicted. A total of 167,693 high quality reads was obtained from Annona muricata and Malus domestica. Clustering on GREENGENES database revealed 570 Operational Taxonomic Units (OTUs). Alpha-diversity indices indicated high diversity and abundance of microbial community. Taxonomic analysis revealed that bacterial community was grouped into 24 phyla and 455 genera. The microbiome of the samples was dominated by distinct populations of four phyla viz Proteobacteria (58.41%), Bacteroidetes (18.59%), Actinobacteria (11.13%) and Firmicutes (7.29%). The functional genes were predicted for 16S rRNA gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG) which indicated amino acid metabolism, carbohydrate metabolism, xenobiotics biodegradation and lipid metabolism, metabolism of terpenoids and polypeptides and biosynthesis of other secondary metabolites as predominant metabolic categories. Thus, the study revealed the structure of microbial community and functional genes composition in A. muricata and M. domestica fruits and this will help to expand the knowledge concerning the structure of plant-associated bacterial communities, revealing valuable information of their impact and indicating their crucial roles in evolutionary and ecological processes.