Haemophilus parasuis is a colonizer of the upper respiratory tract of pigs, although it is better known as the etiological agent of Glässer's disease. Interestingly, several strains can be isolated from a single farm, as determined by both genotyping and serotyping. However, it is not known how an outbreak and the subsequent treatment affect the population of H. parasuis strains. In this study, a farm was studied during an outbreak of Glässer's disease and 1 year after antimicrobial treatment and elimination of clinical signs. Bacterial isolation was attempted from nasal swabs and lesions. After isolation, antimicrobial susceptibility, serotype and genotype were determined. Two different genotyping techniques, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus sequence typing (MLST) were used. The H. parasuis strain that was isolated from lesions during the disease outbreak clustered with other virulent strains by both MLST and serotyping analysis. Nasal isolates were included in the corresponding nasal cluster by MLST, but they presented high variability by serotyping. These nasal isolates included serotypes previously classified as virulent and non-virulent. Finally, we found that during the antimicrobial treatment the diversity of strains isolated in the farm was affected and just one strain, which was resistant to the treatment, was detected. One year after the treatment strain diversity was back to normal (three strains).