The spore morphology and molecular systematic of a new microsporidian which was isolated from the common sea bream Pagrus pagrus (F: Sparidae Linnaeus, 1758) from the Red Sea, Egypt have been studied. Fifty-six out of 300 (18.7%) of this fish were infected with microsporidian parasites. The infection was appeared as whitish, ellipsoid, round, or elongated nodules embedded in the epithelial lining of the peritoneum and also in the intestinal epithelium. Light microscopic study revealed that nodules were encapsulated by a fibrous layer encircling numerous mature spores measuring 1.7 ± 0.6 (1.5-2.7 μm) × 1.5 ± 0.3 μm (1.2-1.8 μm) in size. Ultrastructure of spores was characteristic for the genus Pleistophora: dimorphic, uninucleate spores (each spore possesses three to five polar filament coils) and a posterior vacuole. Also, the early recognizable stages of the parasite within nodules include uninucleated, binucleated, and multinucleated meronts followed by detachment of the plasmalemma of the sporont producing sporoblasts which mature to spores that consist of a spore coat and spore contents. Also, we analyzed the small subunit ribosomal gene (SSUrDNA) using PCR and sequencing specimens from the marine populations of P. pagrus fish from the Red Sea. From blast searches, sequence analysis, and phylogenetic analysis, we did not find corresponding GenBank entries to our species. Comparison of the nucleotide sequences showed that the sequence of our microsporidium was most similar to five Pleistophora species with degrees of identity (>91.5%). It was most similar (97.8% identity) to that of Pleistophora hyphessobryconis (account no. GU126672) differing in 19 nucleotide positions and with lower divergence value, Pleistophora ovariae (96.2% identity, account no. AJ252955), Pleistophora hippoglossoideos (91.9% identity, account no. AJ252953), Pleistophora mulleri (91.9% identity, account no. EF119339), and Pleistophora typicalis (91.9% identity, account no. AJ252956). So, they likely represent new species named Pleistophora pagri sp. n. with accession number JF797622 and a GC content of 53%.