Subclinical (without visible signs) mastitis in dairy cows can be caused by udder infection with staphylococcal bacteria such as Staphylococcus (S.) chromogenes and S. simulans. Little is, however, known about how much the genetics within each of these staphylococci vary. In this study the whole genome of over 100 Swedish milk isolates of each species was sequenced. We found a substantial variation within each staphylococcus in genetic relatedness, presence of virulence factors and antimicrobial resistance. The information improves the understanding of how these bacteria can spread between and within herds and how such infections can be treated and prevented.