Baas Becking stated in 1934 that “Everything is everywhere, but the environment selects”. Following this line of thought, one could attempt, probably unsuccessfully, to replicate a microbial community by copying its environment. For the gut of juvenile animals this would be extremely difficult because its microbiota rapidly evolves during early development. Host and environment both affect the development of the gastrointestinal (GI) microbiota. However, the relative importance of both is too poorly understood to predict accurately microbial composition. Furthermore, even for identically reared individuals, inter-individual variation in gut microbial composition can mask treatment effects. We characterized GI microbiota dynamics of Nile tilapia larvae, reared in two replicate recirculating aquaculture systems (RAS) for six weeks starting with first feeding following yolk sack absorption. To evaluate whether similar temporal and replication effects are also observed in other rearing systems, we also monitored variation in replicated active suspension (AS) systems. Denaturing Gradient Gel Electrophoresis and 454 pyrosequencing of PCR-amplified 16S ribosomal RNA gene fragments showed that variation in GI microbiota between replicate tanks, was not significantly higher than within tank variation. However, when individuals were reared in replicated systems, GI microbiota differed significantly. The highest variation was observed between individuals reared in different system types. Our data suggest that compositional replication of the microbial communities of an ecosystem is practically impossible. We recommend to test the effect of experimental treatments on gut microbiota preferentially in tanks within the same system, rather than between different systems, unless systems within each treatment are replicated.