Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies.