The enteric myxozoan parasites Enteromyxum leei (Diamant, Lom et Dyková) and Enteromyxum scophthalmi Palenzuela, Redondo et Álvarez-Pellitero are responsible for high weight loss in infected fish, which leads to subchronic disease and low mortality rates in gilthead sea bream (GSB), Sparus aurata L., and to high mortality rates in turbot, Psetta maxima (L.). The detection of initial parasite stages in histological sections is particularly difficult, but can be simplified by means of specific antibodies. Rabbit polyclonal antibodies (pAbs) were raised against E. scophthalmi and E. leei, and direct enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry were used to characterize their sensitivity and specificity. Both pAbs were adsorbed (apAb) with non-infected intestines to avoid non-specific labelling of fish tissues and to improve their specificity. The highest titre obtained in ELISA was 1: 32 000 for apAb-Eleei and 1:16 000 for apAb-Escoph. Working dilutions in immunohistochemistry were 1:1000 for apAb-Eleei and 1:8000 for apAb-Escoph. Both apAbs labelled proliferative and sporogonic stages with high specificity. apAb-Escoph was very specific, whereas apAb-Eleei cross-reacted with Sphaerospora dicentrarchi Sitjà-Bobadilla et Álvarez-Pellitero and Sphaerospora testicularis Sitjà-Bobadilla et Álvarez-Pellitero, suggesting the presence of shared antigens. These pAbs stand as new tools for antigenic characterization and the diagnosis of both Enteromyxum species.