Myxozoans are metazoan parasites which are highly pathogenic in commercially importantfish, particularly in aquaculture. Enteromyxosis is an economically significant diseasecaused by the myxosporean parasite Enteromyxum leei.Presently, early diagnosis of enteromyxosis in sharpsnout seabream was achieved bymonitoring fish on a time-scale scheduled basis in combination with a validated moleculardiagnostic technique. Two different successive fish batches of a commercial fish farm weremonitored starting from the first month of on-growing in sea cages until fish reachedcommercial size. Fish weight and water temperature differentially ranged between them.E. leei detection was performed both by classical microscopicobservation of fresh smears and by quantitative polymerase chain reaction (qPCR) whileprevalence, mean intensity and mortality rate were calculated. In total, 520 fish werescreened; 320 from the first batch and 200 from the second one. Parasitosis illustrated aseasonal occurrence pattern (spring and summer). When qPCR was used as a diagnosticmethod, enteromyxosis was diagnosed earlier with more increased prevalence compared to themicroscopic observation. In this case, the parasite was detected at the lowest watertemperature that has ever been recorded (14.7 °C), during the first month of on-growing in sea cages. The two-factorcombination of water temperature and fish weight proved to be the most significant factorthat could determine the emergence and development of parasitosis and smaller fish provedto be more susceptible. Mortality was influenced by both prevalence and intensity ofparasitosis. An earlier diagnosis and identification of all developmental stages of theparasite throughout its life cycle was verified with qPCR, significantly before anyoutbreak occurred. The latter could become a key diagnostic tool for the control ofenteromyxosis, allowing stakeholders and fish farmers to adopt all necessary precautionarymeasures minimizing economic loss in sharpsnout seabream intensive farming.