During the first 2 years of larval rearing trials with Atlantic bluefin tuna, survival was a challenging issue. As bacterial colonization of the gut has been shown to play a key role for other species, we studied the profiles of the microbiota associated with individual larvae at different stages in three distant hatcheries. The Bacterial Community Profile (BCP) was quantified based on PCR-DGGE analyses of partial amplicons from 16S rDNA. Considerable individual variability in BCP was observed before onset of feeding, and the BCP did not show regular fluctuation during ontogenesis. Microalgae were added to the rearing tanks in two of the three hatcheries, but it was not possible to distinguish the effect of location from the effect of algal addition on BCP. In one hatchery, the larvae were reared either with algal addition or in mesocosm, but due to high individual variability, no significant difference in BCP was detected between the two groups. It was hypothesized that this variability was caused by differences in health, physiological status and developmental stage of the larvae. A practical conclusion from the study is the need to analyse a considerable number of individuals to reflect statistically significant differences between the microbial communities associated with rearing groups.