Among other Sparidae species, the gilthead seabream Sparus aurata is the most important fish species in the Mediterranean aquaculture, achieving good growth performances and progressive increased production. However, health management remains as one of the major concerns of the gilthead seabream culture, because diseases can cause major losses to commercial crops. In suboptimal conditions of intensive rearing systems, the danger of disease outbreaks is always present. Since quarantine restrictions were rarely adopted, several microbial pathogens have been transmitted to other geographic locations, and frequently they have colonized new fish hosts and/or new environments. In this work, we have updated some of the most important and also serious pathologies and diseases that from many years ago and presently affect to reared gilthead seabream specimens, mainly those with uncertain or complex aetiology (genetic, nutritional, zootechnic, among others), such as malformations-vertebral deformities, as well as those more classical and emergent parasitic and infectious pathologies and diseases. In addition, avalaible treatment and/or prophylactic measures are also discussed.