A core gut microbiota exists in zebrafish. The study compared gut bacterial communities of zebrafish collected from their natural habitat with those reared in lab facilities. Despite differences in host origin and domestication status, the gut microbiota of domesticated and recently caught zebrafish were strikingly similar, suggesting a shared core microbiota. The zebrafish intestinal environment selects for specific bacterial taxa, regardless of host provenance or domestication status. The gut microbiota of domesticated zebrafish varied among different lab facilities, with variation explained by historical connections between facilities. Pyrosequencing revealed a core microbiota shared among recently caught and domesticated zebrafish, consisting of 21 OTUs, including members of the γ-Proteobacteria, Fusobacteria, Bacilli, Flavobacteria, and Actinobacteria. These shared taxa may constitute a core gut microbiota of the zebrafish intestine. The study highlights the importance of considering historical connections between lab facilities when studying host-microbiota interactions. The results suggest that the gut microbiota of zebrafish is influenced by both environmental factors and host characteristics, with a core microbiota that is common across different locations and domestication statuses. The findings have implications for understanding host-microbiota interactions in zebrafish and other vertebrates.A core gut microbiota exists in zebrafish. The study compared gut bacterial communities of zebrafish collected from their natural habitat with those reared in lab facilities. Despite differences in host origin and domestication status, the gut microbiota of domesticated and recently caught zebrafish were strikingly similar, suggesting a shared core microbiota. The zebrafish intestinal environment selects for specific bacterial taxa, regardless of host provenance or domestication status. The gut microbiota of domesticated zebrafish varied among different lab facilities, with variation explained by historical connections between facilities. Pyrosequencing revealed a core microbiota shared among recently caught and domesticated zebrafish, consisting of 21 OTUs, including members of the γ-Proteobacteria, Fusobacteria, Bacilli, Flavobacteria, and Actinobacteria. These shared taxa may constitute a core gut microbiota of the zebrafish intestine. The study highlights the importance of considering historical connections between lab facilities when studying host-microbiota interactions. The results suggest that the gut microbiota of zebrafish is influenced by both environmental factors and host characteristics, with a core microbiota that is common across different locations and domestication statuses. The findings have implications for understanding host-microbiota interactions in zebrafish and other vertebrates.