Today people are turning to fish as a healthy alternative to red meat. It supplies various essential protein, vitamins, Omega 3 and minerals. It is favored by all people for its delicious taste specially Shrimps and Crabs. However, crustaceans can serve as sources of parasitic infection to man. So this study was planned to estimate prevalence of emerging protozoa among crustaceans. A total of 60 shrimp & crab samples (30 of each) were collected from different markets in Alexandria Governorate. The intestinal contents of each were milked out. Smears were stained with: a) Quick-hot Gram-Chromotrope staining technique (QHG), b) Kinyoun's acid-fast stain (KAF). Microsporidia was encountered in the whole sample of Shrimps and Crabs by both stains (QHG, KAF). In Shrimps; Cyclospora was defected 40% followed by Cryptosporidia (33.3%) by using QHG stain while the results revealed by Kinyoun's acid fast stain were (40%, 80%) respectively. In Crabs; Cryptosporidia was the second encountered protozoa 53.3%, followed by Cyclospora 33.3% as demonstrated by QHG. However, Kinyon's acid fast stain showed 86.7%, 33.3% respectively. The least protozoan parasites shown in the present study were Blastocystis hominis 6.7%, and Dientamoeba fragilis 3.3%, either by QHG or KAF demonstration.