The changes in the histological and three dimensional organizations of lymphoid organ and characteristics of lymphoid cells after chronic infection with yellow head virus (YHV) in Penaeus monodon were investigated. The vascular cast of infected lymphoid organ showed less branching and dramatically shortened terminal capillaries that formed the lymphoid tubules, and only large stumps of these lymphoid tubules remained. This might occur because the terminal ends of the tubules were damaged from YHV infection, as stromal cells and hemocytes in the LT wall were infected and formed foci that could give rise to lymphoid spheroids that broke away from the original lymphoid tubules. Histologically, there was a decrease of PAS-stained connective tissue materials in lymphoid spheroids as well as a decrease of stromal cells as marked by anti-vimentin antibody. This indicated that stromal cells together with type 1 fibers and associated extracellular matrix degenerated in lymphoid spheroids, while type 2 or reticular fibers proliferated and encapsulated the spheroids.