Sarcocystis spp. are cysts-forming coccidian parasites which infect several animals including camels as intermediate hosts. The present study was designed to study the Sarcocystis infection in camels (Camelus dromedaries) at morphological and molecular levels. Sample of the esophageal, heart and ocular muscles tissue were collected from infected camels from El-kharga (New valley Governorate) and examined for Sarcocystis spp. using macroscopic evaluation, light microscopy (LM), transmission electron microscopy (TEM) and molecular analysis. Two species Sarcocystis cameli and Sarcocystis ippeni were recognized. Sarcocysts were thin walled with barely visible projections. Using the TEM, the two structurally distinct sarcocysts were recognized by unique villar protrusions (Vp). Sarcocysts of S. cameli had Vp of type 9j. The sarcocyst wall had upright slender Vp, up to 0.1-0.4 μm long and 0•05-0.1 μm wide. On each Vp, Rows of knob-like protrusions are present appeared to be interconnected. Sarcocystis ippeni had ‘‘type 32'' sarcocyst wall characterized by conical Vp with an electron dense knob. The Vp were approximately 175.27-266.76 nm long, 100.45-175.98 nm wide. In each Sarcocystis, the Vp had microtubules (Mt) that originated at midpoint of the ground substance (Gs) and continued up to the tip. Molecular data revealed the amplification of partial fragments of the 18S rRNA gene (~600 bp). The digestion analysis of obtained PCR products using RFLP method utilizing (Mbo1) appeared 2 bands approximately 250, 350 bp for each Sarcocystis. Molecular analysis demonstared the ability of 18S rRNA gene for distinguishing Sarcocystis species in studied animals and to be used as molecular marker.