East coast fever is a disease of cattle caused by Theileria parva and is transmitted by the tick Rhipicephalus appendiculatus. Buffalos are a natural reservoir of the parasite. The objectives of this study were to determine the T. parva infection in buffalo and cattle field samples, to identify genotypes of T. parva infecting cattle and buffalo and finally to investigate the presence of buffalo-derived T. parva genotypes in cattle that graze in close proximity with infected buffalo. Real-Time PCR (RT-PCR) and Fluorescence Resonance Energy Transfer (FRET) was used to diagnose T.parva. Genotyping of T. parva was conducted by analysing p67, PIM and p104 genes . In addition, amplicons with unique PIM and p104 PCR-RFLP profiles were sequenced to identify shared genotypes. The results have shown the high occurrence of T. parva in buffalo and a much higher occurrence of T. parva in cattle from the Ngorongoro area. Analysis of the variable region of the p67 loci showed four different T. parva alleles in buffalo and cattle. PCR-RFLP analysis of the p104 loci revealed four allelic profiles in buffalo and two in cattle. PCR-RFLP analysis of PIM loci from buffalo gave profiles that were complex and difficult to interpret. On the contrary, cattle showed allelic profiles that resemble Muguga and Marikebuni isolate PIM gene profiles. Multi-locus genotypes (MLGs) and sequence analysis revealed that the majority of buffalo and cattle genotypes were distinct but there is an indication of some sharing of genotypes between buffalo and cattle.