To highlight the importance of the soil-root interface in bacterial root colonization, we performed 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform to characterize the bacterial endophytes of rice plants grown by two experiments – soil and hydroponic, considering their soil, solution, and endosphere compartments. We hypothesized that rice plants from both experiments would exhibit dissimilar endophytic bacterial communities. Alpha-diversity (richness (ASVs), Shannon index, Faith’s phylogenetic diversity, and Pielou’s evenness) for bacterial endophytes was lower in the soil experiment than in the hydroponic experiment. However, the rhizospheric soil exhibited higher microbial diversity and richness than the hydroponic solution after 6 weeks. Proteobacteria and Firmicutes were the most dominant phyla in both experiments, while several other bacterial taxa showed major differences at genus levels. A Venn diagram revealed that 5 overlapping bacterial genera were shared by the endosphere and rhizosphere/solution compartments of both experiments. Principal coordinate analysis (PCoA) based on weighted UniFrac distances showed a clear distinction between microbial communities of all sampled compartments. Furthermore, PERMANOVA results showed that the endophyte communities of both experiments differed significantly (p < 0.001). Overall, this study suggests that the soil-root interface plays a significant role in determining the bacterial endophyte community in rice plants, and the different patterns of endophytic colonization of the rice roots in both experiments were likely influenced by factors that may include bacterial motility, biofilm formation, as well as the decreased effects of root exudates due to dissolution in the solution of the hydroponic experiment.