A large outbreak of hand, foot and mouth disease (HFMD) occurred in Guangdong, China, in 2009. A total of 92,749 cases were officially reported to the Center for Disease Control and Prevention of Guangdong (GDCDC). To clarify the pathogen causing the outbreak, 600 specimens, including stool, rectal swabs, vesicular swabs, cerebrospinal fluid, and throat swabs, were collected from 541 patients and subjected to one-step RT-PCR. Four hundred eighty-nine of 541 patient samples were positive for enterovirus. All positive samples were cultured on RD and Hep2 cells; 307 specimens displayed CPE. Sequence analysis of PCR fragment and typing real-time PCR indicated that these isolates included EV71 (56%), CAV16 (35.5%), CAV6 (2.0%), CAV10 (1.0%), CAV2 (0.7%), CAV4 (1.3%), Echo30 (0.7%), Echo25 (1.0%), Echo4 (0.3%), CBV5 (1.0%) and human rhinovirus (0.7%). 100% (12/12) of fatal cases and 97.2% (140/144) of severe cases carried EV71 and CAV16. The results implied that EV71 and CAV16 were mainly responsible for the outbreak. Comparison with the three global types of EV71 and the five clusters of genotype C showed that the sequences from mainland China (not including the Hong Kong region) are located in subgenogroup C-4 and originate from isolates from the Shenzhen area of Guangdong Province. Results from this study show that the C-4 genotype has been a prevalent pathogen in mainland China since 1998.