The bacterial colonization of a newly hatched fish is known to be important for the larval development and has been found to protect against pathogenic infections. Still, little is known about the early bacterial colonization of fish. We therefore conducted two experiments where we followed the gut and skin microbiota of Atlantic salmon alevins that derived their microbiota from either their eggs (EDM) or lake water (LDM). In the first experiment, we characterized the gut and skin microbiota at 6, 9, and 13 weeks post hatching and investigated the influence of the source for bacterial colonization on the fish’s gut and skin microbiota. In a second experiment, we explored the potential for manipulating the early fish microbiota by addition of two bacterial isolates, and examined the relationship between water and fish microbiota. In both experiments, the fish microbiota were highly dissimilar between the EDM and LDM group. However, both groups were dominated by Pseudomonadales, Burkholderiales and Flavobacteriales. High inter-individual variation and a strong flask effect was observed (especially for the LDM samples). The microbiota changed significantly over time, and bacterial richness increased towards later timepoints. The gut and skin microbiota differed only in the second experiment. The addition of two bacterial isolates at high densities had no significant effects on the microbial community composition indicating resistance against bacterial invasions. In conclusion, we showed that the source microbial community plays an important role in the initial bacterial colonization of Atlantic salmon alevins.