To compare the differences in gut microbiota and antibiotic resistance genes (ARGs) between Litopenaeus vannamei and Macrobrachium rosenbergii, microbiota community structure and microbiota diversity of two shrimps were analyzed by high-throughput sequencing and denaturing gradient gel electrophoresis (DGGE), and 38 kinds of ARGs in the gut bacteria of two shrimps were detected. The effective bacterial sequences of L. vannamei and M. rosenbergii were 42 795 and 40 713. The results showed that the numbers of operational taxonomic units (OTUs) were 124 and 82, and the bacterial types with clear classification status were 5 phyla, 17 genera and 5 phyla, 16 genera. The dominant group in the gut bacteria of L. vannamei is Proteobacteria, which accounts for 75.45%. The dominant genera are Paracoccus (25.83%) and Acinetobacter (25.24%). The dominant group in gut bacteria of M. rosenbergii is Firmicutes (49.74%), and the dominant genera are Lactococcus (49.01%) and Vibrio (29.98%). The Shannon index of the gut bacteria (2.19) of L. vannamei was higher than that of M. rosenbergii (1.78), indicating that the gut bacteria diversity of the former was greater than that of the latter. The analysis results of DGGE fingerprint were consistent with those of high-throughput sequencing, and the bacterial diversity of the two shrimps was significantly different. The PCR results showed that the gut bacteria of L. vannamei carried 15 ARGs and gut bacteria of M. rosenbergii carried 14 ARGs. Our study revealed that the community diversity, OTU richness, total number of species and ARGs in the gut bacteria of L. vannamei were higher than those of M. rosenbergii, which provided a theoretical basis for the subsequent excavation of gut microbial resources.