This study was carried out to evaluate the molecular prevalence of Theileria equi and Babesia caballi in horses from Southern Marmara Region of Turkey and to designate the molecular characterization of the obtained isolates. For this aim between May and July 2012, blood samples were collected from totally 203 horses. After the genomic DNA extractions from blood samples, TaqMan real-time polymerase chain reaction (PCR) analyses were performed with the specific primers which partially amplified the 18S rRNA gene region of B. caballi and T equi. Ten (4.93%) of the examined horses were found to be infected with equine piroplasmosis (EP). The molecular prevalence of T equi and B. caballi in the research area was determined as 2.96% and 1.97%, respectively, without a significant difference (P > .05). No association regarding age, gender, and breed was determined (P > .05) in the prevalence of EP. A total of five samples which were also positive in qPCR assay (four T. equi and one B. caballi) gave amplification on the agarose gel according to the 18S rRNA PCR assay. Thus, conventional PCR showed 66.7% and 25.0% sensitivity for T equi and B. caballi compared with the real-time PCR. Two of four T. equi (BK-1 and BK-2) and one B. caballi (BK-3) PCR-positive isolates were sequenced for the phylogenetic analyses of their partial 18S rRNA gene sequences. BK-1 and BK-2 isolated showed 100.0% identity to each other and were determined in the T. equi genotype E, whereas BK-3 sequence clustered in the B. caballi genotype A. (C) 2015 Elsevier Inc. All rights reserved.