Filter-feeding fish like silver carp and bighead carp have different bacterial communities in their water and intestines. Bighead carp have more diverse bacteria in their bodies compared to silver carp. The types of bacteria present in the two fish species are also different. Silver carp have fewer planktonic bacteria in their intestines. Overall, silver carp have more enriched metabolic pathways in their bodies compared to bighead carp. This study helps us understand how the gut bacteria of these fish can be managed to improve their health and production in aquaculture ponds.