Some species of Sciaenidae were the important fishes in the artificial propagation and breeding in the world. The health of intestinal flora played a significant role in the nutrition, growth and immunity of cultured fishes. However, only a few studies on intestinal flora of cultured croakers have been reported. Investigation of intestinal flora of related species was helpful to the understanding of the influence of host genetic factors on the formation and maintenance of intestinal flora. In order to explore the interspecific structural characteristics, differences of intestinal flora of cultured croakers and the influence of host genetic factors on intestinal microflora, the 16S rDNA V3-V4 region of intestinal microflora was amplified from 5 kinds of yelloe croaker (Larimichthys crocea, Nibea albiflora, N. miichthyoides, Miichthys miiuy, Sciaenops ocellatus) cultured in Sandu Bay, Ningde, Fujian Province and then were sequenced based on Illumina Hiseq2500 sequencing platform. The number of unique tags obtained from these samples were from 20351 to 43347, and the species mentioned above obtained 479, 626, 603, 518 and 556 OTUs, respectively. The classification annotation results showed that they belongded to 33 phyla and 273 genera. Proteobacteria, Bacteroidetes and Firmicutes were the dominant microflora that accounted for about 70% of the total number of the bacteria. The proportion of Spirochetes in the intestinal flora of L. crocea was 26.19%, and it was the dominant flora in the intestinal of L. crocea. Bacillus, Photobacterium, Vibrio, Chryseobacterium, Sphingomonas, and Pseudomonas were the predominant genera of the reared croakers, but great differences in percentages of these genera existed among the microflora of these fish species. The analysis of the microflora diversity of cultured croakers showed that Shannon’s diversity index of the intestinal flora: N. albiflora > N. miichthyoides > S. ocellatus > M. miiuy > L. crocea. The microflora diversity of the intestinal contents of these fishes was higher than that of the intestinal wall. According to the variation analysis of microflora between these species, N. miichthyoides and M. miiuy had the most similar intestinal microflora structure. Then they clustered with the flora of N. albiflora. The intestinal flora of L. crocea was more similar to them than that of S. ocellatus. At the same time, the comparative analysis of the intestinal flora structure showed that the phylogenetic factors were important in the forming of fish’s intestinal microflora. In summary, the intestinal flora of the 5 species of mariculture croakers had core flora with its own characteristics. Although the fishes sampled in this study belonged to relative species and the diets habits were similar, they still had great differences in the intestinal microflora structure. The difference in intestinal flora structure was similar to the phylogenetic relationship between species, which proved that intestinal flora structure was closely related to host genetic factors. Studies on maintaining the intestinal health of aquaculture fish and providing better nutritional feed would improve economic benefits of aquaculture industry. In addition, they can also provide a huge space for the development of new fish feed supplements. This study would provide scientific basis for the development of both feed and probiotics for cultured croakers. In the meantime, the results would be helpful to the control of fish disease and providing relevant experimental evidence on proving host genetics had influence on intestinal flora.