Egypt is the largest producer of farmed mullets worldwide. The mullet seeds are collected from natural waters at the north and northern east of Egypt. Thus, the occurrence of parasitic diseases is relatively high even after being stocked in aquaculture facilities. The current study was conducted on a fish farm located at the coastal area of the Suez Canal region, Egypt. Farmed flathead grey mullet (Mugil cephalus L.) and thin-lipped grey mullet (Liza ramada) showed pinkish-white granular cysts on their body surfaces that measured approximately 5 mm (4–6 mm) in width and 7 mm (5–9 mm) in length and contained a milky coloured exudate. The proximal portion of the fins and apical part of the scales were the only sites of infection. These cysts are randomly scattered throughout the fish body surface. No mortalities were detected among moribund mullets, but these cysts make the fish unsightly, causing commercial rejection. The overall prevalence of infection was 40%. Giemsa-stained wet smears initially indicated that the spores were of Myxobolus species. Subsequently, the phylogenetic analysis of the 18S rRNA gene confirmed the identification of spores as being those of Myxobolus episquamalis. Furthermore, amprolium-salinomycin mixture, which has an established track record for treating myxozoan infections in multiple fish species, was successfully tested in a large-scale field trial. Moribund mullets displayed significant reduction in myxosporean infection following treatment with amprolium-salinomycin mixture. To the best of our knowledge, this is the first report describing the detection of M. episquamalis in farmed flathead grey mullet (Mugil cephalus L.) and thin-lipped grey mullet (Liza ramada) collected from fish farms in the Suez Canal, Egypt.