To evaluate the distribution of most known staphylococcal superantigen (SAg) genes in Staphylococcus aureus isolated from bovine mastitis cases, a genetic analysis of 15 SAg genes and genotypes was performed in a total of 283 S. aureus isolates collected from milk samples of cows with subclinical mastitis in two major diary production regions of China. Almost 65% of the isolates possessed at least one toxin gene. The most frequently found genes were sea (36.0%) followed by sei (31.8%), seg (31.4%) and selm (26.9%). The genes see, selk, or selo were not found in any of the isolates tested. Overall, 28 SAg genotypes were observed, among which the genotypes sea-seg-sei-selm, seg-sei-selm-seln, and sea-sed-selj predominated at the rate of 8.8%, 7.4%, and 6.7%, respectively. Marked geographical variations were noticed in the distribution of individual SAg genes and genotypes among S. aureus isolates from the two different regions. The relationship between toxin genotypes and toxin genes encoding profiles of mobile genetic elements (MGEs) was analyzed, revealing that majority of SAg genes were present in certain MGEs, which were in accordance with current knowledge about MGEs carrying those genes. However, some gene combinations suggest the possibility of the existence of variants or new types of MGEs.