Molecular karyotyping by pulsed field gel electrophoresis was used to characterize Trypanosoma evansi isolates. Ten T. evansi isolates from camels were collected in Eastern and Western Sudan. Isolates from Eastern Sudan which were kept under continuous prophylactic treatment with quinapyramine (Trypacide®), were found to bear a single pattern and belonged to one karyotype group. From Western Sudan where trypanosomosis management was done by individual treatment of proven parasitaemic cases, isolates with diverse karyotype patterns were obtained. This study concluded that the occurrence of karyotype homogeneity amongst T. evansi isolates from field situations where antitrypanosomal compounds have been used may infer the existence of drug-resistance