Hermetia illucens, the so-called black soldier fly (BSF), has been reported as an important insect in treating domestic and agricultural manure wastes. With the ability to live well in the environment of decomposition or waste containing a variety of substances, many types of microorganisms can be related to the intestinal microflora, helping the larvae digest, grow and develop well, even creating protection against parasites and pathogens. The present study aimed to identify the microbial community associated with larvae and determine the dominant species in their intestine. To understand the role of intestinal microflora of BSF larvae for partly explaining the excellent treatment and the ability to live well in the waste environment, denaturing gradient gel electrophoresis (DGGE) and DNA sequencing methods were conducted in three parts of BSF larval intestine. The results indicated that the appearance of 11 dominant bands of larval intestinal microflora. Moreover, by using sequence alignment and phylogenetic analysis, our research has clearly classified seven specific strains of bacteria found in BSF larval intestine including Clostridium amazonese, Clostridium sporogenes, Clostridium tertium, Clostridium saccharolyticum, Actinomycetaceae, Dialister sp. and Dygonomonas. In particular, Clostridium is the most dominant genus compared to other groups and present in all three parts of larval intestine. The results obtained in this study provided insight into the bacterial community composition of black soldier fly larvae that can be used in the environmental, agricultural, and biomedical industries.