Plants harbor diverse and taxonomically structured communities of protective microorganisms that confer beneficial characteristics in plant growth and protection against biotic and abiotic stresses. The aim of this study is to characterize the composition of endophytic bacterial communities in leaves and rhizobacterial communities of the flood affected and unaffected apricot trees by 16S rRNA genes metabarcoding. Results showed a slight bacterial diversity reduction in flood affected condition compared to the unaffected one. The relative bacterial abundance analysis showed that the bacterial taxa were almost uniformly distributed between the leaves. However, a clear differential taxa abundance was observed in rhizosphere soil which may be associated with apricot tree environmental status. In fact, the flood affected rhizosphere soil showed a significant increase in several bacterial taxa including particularly Bacillusfrigoritolerans and Pseudoarthrobacterphenanthrenivorans which are known to be beneficial to soil. However, some Actinobacteria genera that promote growth of plants, including Nocardioidessp.,Streptomycessp.,BlastococcusandGeodermatophilus were decreased in abundance. This distribution of abundance and diversity of the bacterial community in the flood affected tree can be correlated to abiotic stress. These results provide new insights into rhizosphere-associated microbes that are likely playing a crucial role in plant growth and survival.