The importance of this study to investigate some of the myxosporidian and microsporidian parasites infecting economically important marine fish of the Red Sea in Egypt by means of morphologic and morphometric characterization of these parasites, in addition to molecular analysis of their small subunit ribosomal DNA (SSU rDNA) and comparing them with those previously recorded on the GenBank. Also, to characterize some of the important structures of myxo- and microsporidian parasites at the ultrastructural level which are considered as key features for their classification; such as capsulogenesis, valvogenesis and spore morphology (polar capsules, polar filament coils and plasmodial membrane) of the recorded myxozoans. In addition, spore maturation as well as meront formation for the recorded microsporidian parasites were also studied. To clarify the taxonomy of these parasites, the probable phylogenetic relationships as revealed by comparative molecular phylogeny using the SSU rDNA gene sequence were applied and then relate the molecular analyses data of the studied parasites to their ultrastructural characteristics.