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Despite vaccination, cyclical peaks of Bordetella pertussis incidence rates are still observed in Canada and other developed countries, making pertussis one of the most prevalent vaccine preventable bacterial diseases. In the postacellular vaccine era, evolution of bacterial strains has resulted in strains with altered vaccine antigens. Previous Canadian studies have focused on isolates mainly from the provinces of Ontario and Alberta, with only small numbers of isolates from other provinces. Therefore, in this study, we examined a larger sample (n = 52) of isolates from Quebec, Canada, between 2002 and 2014. Isolates were characterized by serotype, sequence type, and prevalence of pertactin deficiency. The Quebec isolates shared characteristics similar to other Canadian isolates and to isolates circulating globally. Although pertactin-deficient isolates were not present, a significant shift in sequence type was observed in more recent years. This study highlights the importance of continually monitoring disease-causing isolates to track evolutionary trends and gain a better understanding of the molecular epidemiology of pertussis in Canada.