This study aimed to determine and evaluate the prevalence of the hidden coccidian tissue parasites (Toxoplasma gondii and Neospora caninum) in camels. For this purpose, 120 blood samples from two breed of camels (60Baldy and 60 Sudani) were collected through a period extend from September 2014 to August 2015. Samples were examined serologically for detection of anti-Toxoplasma gondii antibodies and by using PCR application for detection of Neospora caninum for the first time in Egypt. Results of indirect haemagglutination inhibition (IHAT) revealed that 6 out of 120 (5%) serum samples were seropositive and the infection rate was the highest in both autumn and winter. No significance effect of age (p>0.05) on the prevalence of infection among the examined camels, while the results of indirect Enzyme-Linked Immunosorbent assay (IELISA) showed that 63 out 120 serum sample examined by IHAT were positive (52.5%). Using PCR application of 50 blood samples revealed that 12 (24%) were positive for NC-5 region of Neospora caninum genome. Four positive purified PCR products were chosen randomly and for gene sequencing. The obtained sequences were registered in Gen Bank under accession numbers from MF980926.1 to MF980929.1. The analysis of DNA sequencing revealed that the obtained sequences were related to Neospora caninum with identity ranged from 98 and 99%. we concluded that both ELISA and PCR-sequencing were sensitive methods in the diagnosis of the tissue parasites.