Across taxa, animals with depleted intestinal microbiomes show disrupted behavioral phenotypes. Axenic (i.e., microbe-free) mice, zebrafish, and fruit flies exhibit increased locomotor behavior, or hyperactivity. The mechanism through which bacteria interact with host cells to trigger normal neurobehavioral development in larval zebrafish is unknown. Here, we monoassociated zebrafish with either one of six different zebrafish-associated bacteria, mixtures of these host-associates, or with an environmental bacterial isolate. We found that while the axenic cohort was hyperactive, monoassociation with three different host-associated bacterial species, as well as with the mixtures, resulted in control-like locomotor behavior. Monoassociation with one host-associate and the environmental isolate resulted in the hyperactive phenotype characteristic of axenic larvae, while monoassociation with two other host-associated bacteria partially blocked this phenotype. Furthermore, we found an intriguing inverse relationship between the total concentration of bacteria per larvae and locomotor behavior. These data support a growing body of evidence that individual species of bacteria can have different effects on host behavior, potentially related to their success at intestinal colonization. Specific to the zebrafish model, our results suggest that differences in the composition of microbes in fish facilities could have profound effects on the outcomes of behavioral and pharmacological studies. This dataset is associated with the following publication: Weitekamp, C., A. Kvasnicka, S. Keely, N. Brinkman, X. Howey, S. Gaballah, D. Phelps, T. Catron, T. Zurlinden, E. Wheaton, and T. Tal. Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish. Animal Microbiome. BioMed Central Ltd, London, UK, 3(12): 1-13, (2021).