In order to explore the process and pathology of Thelohanellus wuhanensis diseased Allogynogenetic crucian carp (Carassius auratus gibelio), the disease was divided into four periods of occurrence, development, fade and disappearance according to whether there were mature spores and the degenerated degree of them or not. Pathological observation and analysis of nested PCR were made respectively. Results showed that in the period of occurrence, formed cysts on diseased fish were small and a little uplifted. The cysts were milk white in colour. Trophozoites increased by profilication and no mature spores appeared in the cysts. In the period of development, mature spores appeared in the cysts. Number and size of cysts increased. The cysts were gray black in the colour due to the increase of melanocytes. Diseased fish with higher infection would show death or deformity. In the period of fade, mature spores reduced by flowing out into water through the ruptured gap of cysts or by degenerating gradually until all of them degenerated. At the same time, cysts shrunk and melanocytes were more dense gradually. Diseased fish did not die in the present period due to relieved symptoms. In the period of disappearance, no mature spores and only degenerated materials were left in the flattened cysts. Melanocytes reduced gradually. Finally, the original part of cysts was replaced by connective tissue. Nested PCR analyses showed that the 1 584 bp and 853 bp in the first and second runs of nested PCR were respectively obtained in all of four periods of disease. However, in the late stage of the period of disappearance only 853 bp in the second run of nested PCR was obtained, which illustrated that its quantity reduced. No bands were obtained after late October. Present study not only revealed the pathology of T.wuhanensis infected sides in the four periods of disease, but also defined two ways of the disease fade and disappearance. One way was flow out of mature spores from ruptured cysts into water and another way discovered for the first time was degeneration of mature spores in the cysts.