Abstract: To investigate the intestinal microbial community structure in different species of carp in the aquaponics system, we collected 12 intestine samples of four different species of carp(Ctenopharyngodon idellus, Carassius auratus, Hypophthalmichthys molitrix and Aristichthys nobilis)from the same pond, and investigated their composition and diversity of microbial communities based on high throughput sequencing of 16S rDNA. The dominant microbial genuses were Cetobacterium, Clostridium, Bacteroides and Bacillus; and Cetobacterium and Clostridium were the most abundant core intestinal microbiotas in the four species of carp with different feeding habits in the aquaponics system. The composition, diversity and their relative proportions of these dominant microbial genuses in different species of fish intestinal contents are very similar (P>0.05, Kruskal-Wallis), and the microbiota diversity difference exists between non-dominant microbial genuses in the different species of carp (P < 0.05, Kruskal-Wallis). Moreover, it is showed that feeding habit is not the only key factor that affects the intestinal microbiota of carp with different feeding habits.