Termites are worldwide pests causing considerable damage to agriculture, forestry and buildings. Although physical and chemical methods have been tried to eliminate termite populations, they have the limitations such as low effectiveness, high-toxicity residue, environmentally harmful and high cost. Therefore, it has attracted much attention to develop highly effective, low-toxic, long residual period, environmentally friendly and low-cost termiticidals. Here, we report the characterization and antitermitic activities of a new antitermitic compound-producing endophytic bacterium HUB-I-47 isolated from eastern red-cedar, Juniperus virginiana L. The morphological, physiochemical characteristics of strain HUB-I-47 and its 16S rDNA sequences, and the antitermitic compound were analyzed by gas chromatography-mass spectrometry were studied. We found that the morphology of HUB-I-47 was very similar to that of Bacillus subtilis but presented some differences in shape and cell size. Growth evaluation showed that the lowest, highest, and optimum growth temperatures of HUB-I-47 were 12, 47, and 31°C, respectively, which were different from those of reference strains. The 16S rDNA sequence analysis revealed a high similarity of 99% to those of B. subtilis. Based on these analyses, we named strain HUB-I-47 as B. subtilis subsp. virginiana D. P. Zhou, K. Zhao, J. Liu et W. X. Ping, subsp. nov. This is the first report on the analysis of antitermitic compounds from endophytic bacteria. Our study identified a new resource of antitermitic compounds through endophytic bacteria fermentation.