This report describes outbreaks of histomonosis, a severe disease caused by the protozoan parasite Histomonas meleagridis, which occurred over a period of 3 yr on an organic farm in southern Germany. Among other species, the farm houses layers, broilers, and turkeys. In August 2005 one group of turkeys was naturally infected with H. meleagridis. The strain causing infection was typed by C-profiling as genotype B. A second outbreak occurred 3 yr later. Again, a group of turkeys was naturally infected. The strain causing the infection belonged to genotype A. Two months later one group of broilers became infected with H. meleagridis type B and a group of turkeys with H. meleagridis type A. Four weeks later two further groups of broilers showed symptoms. DNA of H. meleagridis was detected but genotyping was not possible. In conclusion, genotyping of the histomonal strains causing the disease showed that at least two different histomonal strains caused the outbreaks and that the strains circulated on the farm at the same time.