In sturgeon aquaculture, abnormal growth variations among fish in the same pond frequently result in decreased yields. The gut microbiota, a crucial component of the digestive system, plays a pivotal role in growth performance of these fish. Currently, there is limited research on the relationship between gut microbiota and individual growth differences in sturgeon. The objective of this study was to examine the characteristics of the gut microbiota in populations of Huso dauricus and Acipenser schrencki in which growth rate differences exceeded 50% of body weight. The fish were bred at the same time and under identical conditions. The aim was to uncover the relationship between sturgeon growth rate and the composition of the gut microbiota. The results revealed notable differences in gut microbiota diversity and composition between H. dauricus and A. schrencki, as well as among different populations in both species. In the fast-growing population of H. dauricus (LH), the dominant genus in the gut was Sphingomonas (67.0%), whereas in the slow-growing population of the same species (SH), the dominant taxa were Sphingomonas (29.5%) and Clostridium sensu stricto 1 (54.2%). In the fast-growing population of A. schrencki (LA), the dominant genera in the gut were Sphingomonas (33.5%) and Cetobacterium (38.1%), whereas in the medium-growing population of the same species (MA), the dominant taxa were Sphingomonas (42.6%), Clostridium sensu stricto 1 (14.3%), and Cetobacterium (33.0%). Sphingomonas and Clostridiaceae were the primary discriminatory taxa in the gut microbiota of sturgeon exhibiting varying growth rates. In conclusion, species-specific variations were evident in the diversity and composition of the gut microbiota in sturgeon. Genetic factors play a crucial role in shaping and selectively altering the gut microbiota in animals, including fish. Moreover, each individual fish harbors a distinctive ecosystem within its gut, which is influenced by genetic factors and contributes, to some extent, to the determination of the types and quantities of gut microbiota. There is evidently a close relationship between the gut microbiota and fish growth, as the gut microbiota directly or indirectly impacts the growth rate of the fish through its involvement in digestion, immunity, and metabolism. In particular, Sphingomonas and Clostridiaceae may exert a pivotal influence on sturgeon growth rates. These findings provide initial insights into the link between the gut microbiota of sturgeon and growth rates, offering a theoretical foundation for the precise modulation of the intestinal microbiota to attain rapid growth of sturgeon in aquaculture.