Objective Using healthy female reproductive-age rhesus macaques as the research subjects,we explored the correlation between menstrual cycle abnormalities and gut microbiota composition by using 16S rRNA metagenomic sequencing.Methods Twenty-seven healthy female rhesus macaques were divided into regular menstrual and irregular menstrual groups.Fecal samples were collected at follicular phase(FP),ovulation phase(OP)and luteal phase(LP)of the two groups.The structure and diversity of bacterial flora in different physiological periods were analyzed and compared between the two groups.Results At the phylum level,Firmicutes,Bacteroidetes,and Proteobacteria dominated the sample flora in the follicular,luteal,and ovulatory phases of the rhesus macaques in both the regular and irregular groups,with a combined percentage of more than 98% .At the genus level,the genus Prevotella_9,Ruminococcaceae_UCG-002,Lactobacillus,Prevotella_2,Phascolarctobacterium,Ruminococcaceae_UCG-005,Streptococcus,Blautia,Prevotellaceae_NK3B31_group,Rikenellaceae_RC9_gut_group were dominant.In the luteal phase the percentage of Firmicutes was higher in the regular group than in the irregular group,while the opposite was true for Bacteroidetes.Spirochaetes were higher in the regular group than in the irregular group at all 3 stages(P＜0.05).Conclusion There were some differences in intestinal microbial composition between the two groups of macaques with regular and irregular menstrual cycles,which provided some reference for the study of intestinal bacteria and ovulation disorders.