An increased incidence of Mycoplasma pneumoniae infections was reported in 2011 in two cities in France, Bordeaux and Caen. Two complementary molecular typing methods, PCR-RFLP on adhesin P1 and multilocus variable number tandem repeat analysis (MLVA), were used to determine whether this phenomenon was clonal. In 2011, the percentage of M. pneumoniae-positive patients doubled in both cities compared with 2010. Macrolide resistance remained stable at 8.3% of patients. Eighteen MLVA types were identified among 94 M. pneumoniae-positive specimens, demonstrating that the phenomenon was multiclonal. Types P, J, U, X and E were the most frequent and 81.6% of the strains were adhesin P1 type 1.