After the first outbreak of fatal Mycoplasma ovis infection (eperythrozoonosis) in a sheep flock in Hungary (1997), a second wave of the disease was noted in 2006, with different seasonal pattern and affected age group, as well as increased mortality (5.5%). The aim of the present study was to molecularly characterize the causative agent and to reveal underlying factors of the second wave of the disease. Remarkably, among the 33 sheep examined, 17 were infected with two strains of haemotropic mycoplasmas. Cloning and sequencing isolates of the latter showed that one of the strains was 99.4-99.8% identical to M. ovis (AF338268), while the second was only 96.8-97.9% identical and contained a 17-bp deletion. Different isolates of both strains were demonstrated in the same animal. When analyzing possible risk factors for fatal disease outcome, we found that among sheep born prior to the 1997 outbreak significantly more animals survived the second outbreak than succumbed to disease. In addition, locally born sheep were less frequently diseased than sheep introduced into the flock from other places. This suggests an immunoprotective effect in some animals. Concurrent infection with Anaplasma ovis was detected in 24 of the 33 evaluated sheep. In conclusion, this is the first study to demonstrate the existence of and characterize two genetically distinct ovine haemotropic mycoplasma strains in a sheep flock with fatal haemolytic anaemia.