The thymus in teleost fishes plays an important role in producing functionally competent T-lymphocytes. However, the thymus in tilapia is not well known, which greatly hampers investigations into the immune responses of tilapia infected by aquatic pathogens. The histological structure and ultrastructure of the thymus in Oreochromis niloticus, including embryos and larvae at different developmental stages, juveniles, and adult fish, were systematically investigated using whole mount in situ hybridization (WISH), and light and transmission electron microscopy (TEM). The position of the thymus primordium was first labeled in the embryo at 2 days post-fertilization (dpf) with the thymus marker gene recombination activating gene 1 (Rag1), when the water temperature was 27 °C. Obvious structures of the thymus were easily observed in 4-dpf embryos. At this stage, the thymus was filled with stem cells. At 6 dpf, the thymus differentiated into the cortex and medulla. The shape of the thymus was 'broad bean'-like during the early stages from 4 to 10 dpf, and became wedge-shaped in fish larvae at 20 dpf. At 6 months post-fertilization (mpf), the thymus differentiated into the peripheral zone, central zone, and inner zone. During this stage, myoid cells and adipocytes appeared in the inner zone following thymus degeneration. Then, the thymus displayed more advanced degeneration by 1 year post-fertilization (ypf), and the separation of cortex and medulla was not observed at this stage. The thymic trabecula and lobule were absent during the entire course of development. However, the typical Hassall's corpuscle was present and underwent degeneration. Additionally, TEM showed that the thymic tissues contained a wide variety of cell types, namely lymphocytes, macrophages, epithelial cells, fibroblasts, and mastocytes.