In order to provide science-based information for the control of cow mastitis, to understand the genetic polymorphisms of dairy-sourced Staphylococcus aureus, we conducted genotyping of Staphylococcus aureus isolates from milk samples collected from cows with clinical mastitis using the random amplified polymorphic DNA (RAPD) method with three oligonucleotide primers. In total, 177 Staphylococcus aureus isolates were obtained from dairy farms in 5 different provinces in China, including Guizhou, Inner Mongolia, Shanghai, Sichuan, and Gansu. The results showed that the amplified product bands with three primers per isolate ranged from 1~9 and the product sizes from 240 to 4,500 bp. Primer OLP13 had the highest discriminant coefficient. The Staphylococcus aureus strains were divided into 11 genotypes by fingerprint with oligonucleotide primers OLP13. There were 12 strains in type 1, 8 in each of types 2 and 5, 22 in each of types 3 and 7, 13 in types 4, 11 in type 6, 25 in type 8, 28 in type 9, 8 in type 10 and 5 in type 11. Among the 11 types of S. aureus isolates, type3 (14/37) and type 7 (15/35) were the main prevalent strains in Guizhou and Inner Mongolia Province respectively. Type 9 (21/55) had the highest prevalence rate and type 8 (10/55) was higher than other types in Shanghai, both of them were closely related. The results showed that the genotype distribution in various regions was noticeably different. Differences in dairy farming practices, geographical environments, and the use of antibiotics may be the reasons for the varied distribution of different genotypes in those provinces.