The purpose of this study was to determine the prevalence of clinical, subclinical and chronic infection with the equine parasite T. equi in some Egyptian localities (Cairo and Giza governorates). A panel of 396 equine blood samples representing 141 horses, 250 donkeys and 5 mules was collected from equines during the period from April 2015 to March 2016 using microscopic examination and conventional PCR. Microscopically a twenty two (5.56%) of 396 were positive for T. equi merozoites that appeared as small rounded, pyriform shaped and maltase cross shaped merozoites. Among 8/141(5.67%) horses and 14/250 (5.60%) donkeys were found to have positive for T.equi. A one hundred blood samples (45 horses, 50 donkeys and 5 mules) selected randomly were also examined by PCR. The results of PCR showed 30/100(11/45 (24.4%) horses, 18/50 (36%) donkeys and 1/5 (20%) mule) were positive for T.equi. When the sequenced PCR amplicons (n=3) were aligned to the reference nucleotide sequences of T. equi accessed in Genbank, the horse isolate showed insertion of Thymine (T) base at position 23 and substitution of Thymine (T) base with Cytosine (C) base at position 91, while the donkey and mule isolates have no alterations when compared to the reference sequences. The phylogenetic analysis showed that the sequenced PCR isolates belonged to T. equi. The obtained sequences were deposited in the GeneBank database under accession numbers MF192854, MF192855 and MF192856.