In August 2002, bovine anaplasmosis and concurrent infections with Mycoplasma sp. and piroplasms were reported in a cattle herd in an alpine region of Switzerland. The piroplasms were identified by PCR/sequencing of part of the 18S rRNA gene as Babesia bigemina and Theileria of the buffeli/sergenti/orientalis-complex, which have never been diagnosed in Switzerland before. The B. bigemina isolate was genetically characterised at two loci and compared with isolates from Italy, Spain, Turkey, Kenya and Mexico. Analysis of the internal transcribed spacer 2 (ITS2) of the rRNA genes revealed high polymorphism not only among the isolates but even within the isolates, and the presence of two types of the ITS2 in every isolate was confirmed. A dendrogram based on ITS2 sequences showed that the Swiss isolate was most closely related to a Spanish isolate but no sequences of the isolate from Switzerland were identical to any of the other isolates. The isolate from Italy was not positioned in the same cluster as the Swiss and the Spanish isolate. This had been anticipated as the nearest known endemic area of B. bigemina in Central Italy. Sequence analysis of the rhoptry-associated protein-1c gene (rap1c) confirmed the similarity of the Swiss and Spanish isolate. Hence, our molecular analyses of the Swiss B. bigemina isolate did not unequivocally track its geographical origin and the way of introduction remains obscure.