Mesanophrys sp. is reported to be highly pathogenic to marine crustaceans. This study presents the first report of Mesanophrys sp. infection in the mud crab (Scylla paramamosain). In this study, we first recorded the survival rates of an experimentally infected group and a control group; the cumulative survival rate in the infected group was significantly lower compared to the control group after 72 h (73.20% vs. 94.19%), while the highest mortality of S. paramamosain occurred within the first 24 h post-infection. Then, we investigated the dynamic distribution and tissue tropism of the Mesanophrys sp. in the infected S. paramamosain by a quantitative real-time polymerase chain reaction (qPCR). The result showed that a significant increase in the number of Mesanophrys sp. could be detected in all tested tissues (obtained from the eyestalks, gills, heart, nerves, muscles and hepatopancreas) at 3 h post-infection. The numbers of Mesanophrys sp. in the gill, eyestalk and nerve tissues were relatively higher than in the other tissues. The gill tissue showed the highest numbers from 6 to 48 h. Histopathological observation found a severe collapse in the filament structure, which indicated tissue-specific pathogen infection. Furthermore, the antioxidant enzyme activity of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in three representative tissues (gill, muscle and hepatopancreas) were compared between the infected and control groups, and a significant increase in enzyme activity was observed in all three tested tissues in the infected group, indicating a relatively strong innate immune defense reaction that could have been induced by Mesanophrys sp. infection. These results will be helpful to Mesanophrys sp. pathogenicity-related research and the control of this pathogen in S. Paramamosain in the future.