The molecular characteristics of 480 Mycoplasma pneumoniae polymerase chain reaction-positive specimens (331 were previously reported and 149 were newly reported) collected from pediatric patients in Beijing, China, between 2003 and 2015 were analyzed. Genotype M4-5-7-2/P1 were the most prevalent across the 13-year study period, although the isolation and mutation rates for this genotype varied between the periods 2003-2007, 2008-2013, and 2014-2015. In addition, there was a close association between the M4-5-7-2 genotype and macrolide resistance.