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The gut microbiota is contributable to the adaptation and health of deep-sea organisms and has been revealed to be affected by many factors, especially the host species and diet. Here, we employed high-throughput sequencing of 16S rDNA to compare the gut microbial composition and diversity of two hadal amphipod species, Hirondellea gigas and Halice sp. MT-2017, which are predominant inhabitants in the Challenger Deep. Results showed that Tenericutes and Proteobacteria were the most abundant phyla, occupying more than 50% of total phyla, across all the specimens. At genus level, “Candidatus Hepatoplasma” was overall dominant, followed by Psychromonas in H. gigas and Psychrobacter in Halice sp. MT-2017 respectively. Notably, though two hadal amphipod species shared the same predominant symbiont of genus “Ca. Hepatoplasma”, they were classified into two different OTUs, which suggested that the colonization of symbionts were host-specific. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was still a significant divergence of gut microbiota between two hadal amphipod species, which dwelled in the same extreme environment. Altogether, the results dropped a hint to the importance of symbiont genus of “Ca. Hepatoplasma” to amphipod survival in the hadal zone.