Histozoic parasite-fish host interaction is a dynamic process that leads to the formation of a granuloma, a specific chronic inflammatory response with discernible histological features. Mullets (Osteichthyes: Mugilidae) represent a suitable model concerning the development of such lesions in the host-parasite interface. The present work aimed to identify granuloma developmental stages from the early to the late phase of the infection and to characterize the immune cells and non-inflammatory components of the granuloma in different stages. For this purpose, 239 mullets were collected from 4 Sardinian lagoons, and several organs were examined by combining histopathological, bacteriological, and immunohistochemical methods. Granulomas associated with trematode metacercariae and myxozoan parasites were classified into three developmental stages: (1) pre-granuloma stage, characterized by intact encysted parasite and with no or mild tissue reaction; (2) intermediate stage, with partially degenerated parasites, necrosis, and a moderate number of epithelioid cells (ECs); and (3) late stage, with a necrotic core and no detectable parasite with a high number of ECs and fibroblasts. The three-tier staging and the proposed morphological diagnosis make it conceivable that histopathology could be an essential tool to evaluate the granulomas associated with histozoic parasitic infection in fish.