Myxozoans can induce losses in production of marine and freshwater fish. Recently, a new parasitic myxozoan species, Sinuolinea niloticus, was identified and its importance highlighted. This study aimed to investigate Sinuolinea niloticus and its macroscopic and microscopic alterations in Nile tilapia (Oreochromis niloticus) specimens from fish farms in Botucatu, São Paulo, Brazil, as well as its molecular detection. Thirty tilapias from three different fish farms were collected and submitted to necropsy examination, where organs were sampled for histopathological and molecular analysis. The main necroscopic findings at all three fish farms were hemorrhaging, fin erosion, hepatomegaly, and splenomegaly. Microscopically, the main findings were degeneration of hepatocytes and hepatitis, epithelial and goblet cell hyperplasia in the gills, nephritis, gastritis, and presence of myxozoan-like structures in different organs. S. niloticus, detected by qPCR, showed a 90% prevalence among surveyed fish at farm 1 and 100% at farms 2 and 3. The high prevalence found in this study shows the importance of this myxozoan as a potential pathogenic agent of farmed O. niloticus that negatively affects fish health and, consequently, production.