To determine the variation in the PantonValentine leukocidin (PVL) gene sequences and different PVL-encoding phages of Staphylococcus aureus strains collected from children in mainland China, fifty-eight strains with PVL collected from 2007 to 2009 were used. Their molecular characteristics were examined. Primers were designed to sequence the PVL genes. Six PVL-encoding phages (?PVL, ?108PVL, ?SLT, ?Sa2MW, ?Sa2958, and ?Sa2USA) were identified by PCR. Eleven sequence types (ST) were detected with ST59 (39.7%, 23/58) the most frequent ST, followed by 910 (22.4%, 13/58), and 338 (12.1%, 7/58). Single nucleotide polymorphisms (SNP) were identified at 11 locations in the PVL genes. SNP (nucleotide 1396, A?G) and SNP (nucleotide 1546, A?G) were observed in >10 sequences. Four additional SNP were non-synonymous. Both SNP (nucleotide 16, C?A) and SNP (nucleotide 62, C?T) were present in the same ST59 strain. SNP (nucleotide 527, A?G) was present in five strains belonging to ST30, 121, 1, and 93. SNP (nucleotide 1436, A?C) was present in one ST30 strain. Fifteen strains belonging to ST910, ST217, and ST30 carried a PVL phage that had an icosahedral head morphology. Nine ST59 strains carried ?108PVL. Three ST88 strains carried a PVL phage that had an elongated head morphology. Twenty-seven strains, including 60.9% (14/23) of ST59 and all ST338 strains, had no detectable phage. In conclusion, sequence variation in PVL genes and PVL-encoding phages was generally related to the lineage. ST59 strains may indeed carry novel PVL phages.