Fresh produce vegetables are colonized by different bacterial species, some of which are antagonistic to microbes that cause postharvest losses. However, no comprehensive assessment of the diversity and composition of bacteria inhabiting surfaces of fresh pepper plants grown under different conditions has been conducted. In this study, 16S RNA amplicon sequencing was used to reveal bacterial communities inhabiting the surfaces of red and green pepper (fungicides-treated and non-fungicides-treated) grown under hydroponic and open field conditions. Results revealed that pepper fruit surfaces were dominated by bacterial phylum Proteobacteria, Firmicutes, Actinobacteria, and, Bacteroidetes. The majority of the bacterial operation taxonomic units (97% similarity cut-off) were shared between the two habitats, two treatments, and the two pepper types. Phenotypic predictions (at phylum level) detected a high abundance of potentially pathogenic, biofilm-forming, and stress-tolerant bacteria on samples grown on open soils than those from hydroponic systems. Furthermore, bacterial species of genera mostly classified as fungal antagonists including; Acinetobacter, Agrobacterium, and Burkholderia were the most abundant on the surfaces. These results suggest that peppers accommodate substantially different bacterial communities with antagonistic activities on their surfaces, independent of employed agronomic strategies and that the beneficial bacterial strains maybe more important for peppers established on open fields, which seems to be more vulnerable to abiotic and biotic stresses.