Abstract: 【Objective】 Metagenomic sequencing was adopted to reveal the gut microbiota composition and antibiotic resistance of Akhal-Teke horses and Yunnan dwarf horses， which could provide theoretical basis for clarifying the maintenance mechanism of equine gut microbiota and developing targeted microecology regulation strategies.【Method】 Ten fresh fecal samples each from Akhal-Teke horses and Yunnan dwarf horses were collected. Total microbial DNA was extracted and metagenomic sequencing was performed. Metagenomic assembled genomes （MAGs） were obtained through sequence assembly and binning， followed by species annotation and phylogenetic construction. The types， relative abundance， and distribution patterns of antibiotic resistance genes （ARGs） were identified using the CARD database. Functional analysis of phage accessory metabolic genes （AMGs） was performed using VIBRANT， and phage-host interaction relationships were predicted using CRISPR-spacer matching technology.【Result】 The dominant gut floral phyla of both Akhal-Teke horses and Yunnan dwarf horses belonged to Firmicutes and Bacteroidetes， with additional phyla such as Spirochetes， Fibrobacteria， and Verruciformis. At the genus level， there were differences in species composition between different breeds. LEfSe analysis at the phylum level showed that Fibrobacteria was significantly enriched in the gut flora of Yunnan dwarf horses （P<0.05， the same below）， and Methanogenic Archaea was also significantly enriched in the gut flora of Akhal-Teke horses. Obvious relative abundance differences were observed in some MAGs between Akhal-Teke horses and Yunnan dwarf horses， indicating a clear separation in the overall gut flora structure. The ARGs profiles of Akhal-Teke horses and Yunnan dwarf horses were clearly separated. Antibiotic resistance genes lnuC， tet_44， ACl-1， CfxA， and CfxA6 were relatively abundant in Yunnan dwarf horses， while OXA-347， tetO， poxtA， and tet32 were relatively abundant in Akhal-Teke horses. The genes contained resistance to cephalosporins and tetracyclines were commonly found in the gut of both breeds of horses.【Conclusion】 The gut microbiota composition of Akhal-Teke horses and Yunnan dwarf horses exhibits obvious breed specificity， characterized by the conservation of the core flora of Firmicutes and Bacteroidetes， the coexistence of breed-specific microbial groups， phages， and antibiotic resistance genes. The host genetic background and shared rearing environment jointly shape the structure and function of the gut microecology of Akhal-Teke horses and Yunnan dwarf horses.