Background: Ticks are notorious vectors of various pathogenic protozoa, bacteria, and viruses that cause serious and life-threatening illnesses in humans and animals worldwide. Screening of ticks for such pathogens by using molecular tools may identify the prevalence of tick-borne pathogens in particular geographic environments. Babesia are tick-transmitted protozoa that comprise some of the most ubiquitous and widespread parasites of erythrocytes in humans and a wide range of wild and economically valuable domestic animals such as cattle and horses. For transmission to occur, therefore, the Babesia parasite must complete an elaborate developmental programme in the hostile tick environment.Objectives:To investigate molecular epidemiology of babesiosis in ticks from different ecological areas isolated in MongoliaSpecific objectives are:1. Molecular identification of tick-borne pathogens by multiplex PCR2. Analysis of molecular epidemiology focused on babesiosis in ticks from different ecological areas3. Determination of transmission ticks’ species of babesiosis Materials and Methods: A total of 528 ticks, including 5 species from three genera (D. nuttalli, D. niveus, D. silvarum, I. persulcatus and H. asiaticum), were collected from domestic animals, from humans, or by flagging of the vegetation at sites from 10 different provinces in Mongolia. 360 individual ticks were examined by multiplex PCR to detect DNA of tick borne pathogens. The multiplex PCR primers were specific to E. canis VirB9, Babesia spp 16S rRNA and H. canis 16S rRNA genes. At the final concentration each reaction was 25 μl. Results: DNA extraction was successful in 360 of these ticks. Babesia spp. were detected in 145 out of the 360 investigated ticks of all five tick species. Multiplex PCR products were from D. nuttalli, D. niveus, D. silvarum, I. persulcatus and H. asiaticum collected from horses, sheep, goats, camels, and cattle were identified as Babesia spp. The prevalences of babesiosis were in Тuv 2.1% (3/145), Dornogobi province 3.4% (5/145), Selenge 3.4% (5/145), Zavkhan 4.1% (6/145), Аrkhangai 6.9% (10/145), Bulgan 8.3% (12/145), Khovd 13.8% (20/145), Bayankhongor province 17.9% (26/145), Gobi-Altai 18.6% (27/145), Khuvsgul 21.4% (31/145) respectively.Conclusion:1. The infection rates of babesiosis were 40,2% by multiplex PCR2. The prevalences of babesiosis were in forest and forest-steppe 39.3%, forest-steppe and steppe 38.6%, gobi and desert 22% respectively.3. H. аsiaticum, I. persulcatus, D. niveus, D. silvarum, D. nuttalli play an important role as a vector of babesiosis.