Although Anaplasma marginale was known to be endemic in Italy, the diversity of Anaplasma spp. from this area have not been characterized. In this study, the prevalence of Anaplasma spp. antibodies in randomly selected farm animals collected on the island of Sicily was determined by use of a MSP5 cELISA for Anaplasma spp. and an immunofluorescence test specific for Anaplasma phagocytophilum. Genetic variation among strains of Anaplasma spp. from animals and ticks was characterized using the A. marginale msp1alpha and the Anaplasma spp. msp4 genes. Eight species of ticks were collected and tested by PCR. Seropositivity for Anaplasma spp. and A. phagocytophilum was detected in bovine and ovine samples. All the donkeys were seropositive for A. phagocytophilum but not for Anaplasma spp. Four A. marginale genotypes were identified by msp4 sequences from bovine and tick samples. Two new genotypes of Anaplasma ovis were characterized in sheep. The sequences of A. phagocytophilum from three donkeys proved to be identical to the sequence of the MRK equine isolate from California. Six A. marginale genotypes were found in cattle and one tick using the A. marginale msp1alpha sequences. All genotypes had four repeated sequences in the N-terminal portion of the MSP1a, except for one that had five repeats. The Italian strains of A. marginale contained three repeat sequences that were not reported previously. Definition of the diversity of Anaplasma spp. in Sicily reported, herein is fundamental to development of control strategies for A. marginale, A. ovis and A. phagocytophilum in Sicily.