Abstract: As one of the most important economic animals in China, red swamp crayfish (Procambarus clarkii) has been in short supply in recent years, and the market has put forward higher requirements for the production and quality of red swamp crayfish. To study the intestinal microbiota in red swamp crayfish at different sexes and stages of growth, we collected male and female adult crayfish of (27.00±1.50) cm in length from the natural environment and larval crayfish of (2.00±0.20) cm in length from lab, respectively, 16S rRNA high-throughput sequencing. The results showed that there were no significant difference in the diversity or function of the intestinal microbiota between different sexes, and the composition was relatively consistent (Independent sample t-test, P>0.05). The dominant bacterial phyla included Firmicutes, Proteobacteria and Bacteroidetes, and bacterial genera included Bacteroidia, Shewanella, Clostridium and Citrobacter. The abundances of dominant bacterial groups varied greatly among individuals. These dominant bacterial groups tended to be conservative in adult crayfish intestine as resident microorganisms. The analysis of Beta diversity showed that male and female crayfish samples were not clustered separately, which indicated no significant difference between male and female crayfish. Among the intestinal microbiota at different growth stages, the Alpha diversity indexes of intestinal microbiota in larval crayfish were significantly higher than those in adult crayfish (Independent sample t-test, P<0.05). In terms of the composition and structure at the phylum level, the dominant bacterial groups in two stages were relatively consistent, including Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. The ratio of Firmicutes to Bacteroides in adult crayfish was higher than that in larval crayfish, indicating that the adult crayfish has a greater potential to digest foods and absorb nutrients. At the genus level, the composition of the dominant genera in the two stages of growth were quite different. The dominant genera of larval crayfish included Unclassified_Burkholderiales (21.1%), Hydrogenophaga (7.6%), Flavobacterium (7.4%), Unclassified_Comamonadaceae (5.4%) and Alkaliphilus (5.2%). The dominant genera of adult crayfish included Bacteroidia (12.5%), Flavobacterium (10.8%), Paracoccus (9.1%) and Unclassified_ Lachnospiraceae (5.5%). The top 20 most diverse genera of adult and larval crayfish included Mycoplana, Asticcacaulis, Sphingomonas, Alkaliphilus, Novosphingobium, Methylopila, Sphingobium, Dyadobacter, Rhodococcus, Hydrogenophaga, Mycobacterium, Tepidibacter, Demequina, Kaistobacter, Ancylobacter, Delftia, Ochrobactrum, Rheinheimera, Methyloversatilis and Sediminibacterium. A large number of Flavobacterium, Bacteroidetes and Hydrogenophaga in the intestines of adult and larval crayfish help the body to carry out a variety of nutrient metabolisms and there were more bacteria related to carbohydrate metabolism in adult crayfish. The Beta diversity of intestinal microbiota showed that adult and larval crayfish samples were clustered separately in PCA analysis, PCoA analysis, NMDS analysis, UPGMA cluster analysis and PLS-DA analysis, indicating great difference between adult and larval crayfish. In addition, the analysis of Adonis/PERMANOVA showed significant difference in the intestinal microbiota between adult and larval crayfish. PICRUSt function prediction showed that the relative abundance of nutrient metabolism function was the highest in the functions of intestinal microbiota in crayfish. The dominant functions of intestinal microbiota in adult crayfish included membrane transport and carbohydrate metabolism, the dominant functions of larval crayfish included cell movement, biodegradation and metabolism of xenobiotics and lipid metabolism. The abundance of metabolizing carbohydrates in adult crayfish was significantly higher than that of larval crayfish. During the breeding cycle of red swamp crayfish, the diet habits will change from plankton to granular feed as the development of crayfish. The capacity of secreting various digestive enzymes in the intestine is enhanced, accompanied by the changes of intestinal microbiota in composition and function to adapt to the shift in diet habits. Our results provide reliable data support and theoretical guidance for the subsequent improvement of the production and quality of red swamp crayfish, the selection of intestinal probiotics and the study of probiotic preparations.