In order to study the adaptation scope of the fish respiratory organ and the O2 metabolism due to endurance training, we subjected adult zebrafish (Danio rerio) to endurance exercise for 5 weeks. After the training period, the swimmer group showed a significant increase in swimming performance, body weight and length. In scanning electron microscopy of the gills, the average length of centrally located primary filaments appeared significantly longer in the swimmer than in the non-trained control group (+6.1%, 1639 μm vs. 1545 μm, p = 0.00043) and the average number of secondary filaments increased significantly (+7.7%, 49.27 vs. 45.73, p = 9e-09). Micro-computed tomography indicated a significant increase in the gill volume (p = 0.048) by 11.8% from 0.490 mm3 to 0.549 mm3. The space-filling complexity dropped significantly (p = 0.0088) by 8.2% from 38.8% to 35.9%., i.e. making the gills of the swimmers less compact. Respirometry after 5 weeks showed a significantly higher oxygen consumption (+30.4%, p = 0.0081) of trained fish during exercise compared to controls. Scanning electron microscopy revealed different stages of new secondary filament budding, which happened at the tip of the primary lamellae. Using BrdU we could confirm that the growth of the secondary filaments took place mainly in the distal half and the tip and for primary filaments mainly at the tip. We conclude that the zebrafish respiratory organ-unlike the mammalian lung-has a high plasticity, and after endurance training increases its volume and changes its structure in order to facilitate O2 uptake.