The value of polymerase chain reaction (PCR)-based DNA fingerprinting and plasmid profile analysis for differentiation of Histophilus ovis isolates was assessed. Nineteen isolates of H. ovis were typed by PCR-ribotyping, repetitive extragenic palindromic element (REP)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR. These methods distinguished five types by PCR-ribotyping, 11 types by REP-PCR and seven types by ERIC-PCR. The ribotyping method produced a relatively simple pattern and a small number of distinct types and was useful for differentiation of H. ovis from the phenotypically similar organism, Haemophilus somnus. REP- and ERIC-PCR both produced complex banding patterns, but increased the discrimination between strains. Plasmids were found in 12 of the 19 isolates and there were four different plasmid profiles. A combination of the PCR methods and plasmid profile analysis provided a high resolution typing method for H. ovis.