Bovine mastitis, an inflammation of the udder usually caused by bacteria, is the most common disease in dairy cattle worldwide with a negative economic impact on the dairy industry. In this study 3020 quarter milk samples from 647 dairy cows on 166 Austrian farms were collected and microbial species, spa type for Staphylococcus (S.) aureus and antimicrobial susceptibility were analysed. A multinomial logistic regression model was applied to investigate the effect of possible categorical influencing covariates on the microbiological findings. Additionally, a generalized linear model was used to analyse the effects of genotype and pathogen species on the occurrence of antimicrobial resistance. Staphylococci were the most common (17% of samples) udder pathogens including 32 different S. aureus spa types. The occurrence of pathogen groups was significantly associated with the clinical mastitis score. Enterobacteriaceae isolates had a significantly higher probability of being present in severe mastitis cases compared to streptococci. Benzylpenicillin and tetracycline were the most common resistance in S. aureus including 14% and 11% resistant isolates. Whereas 16% and 13% of coagulase-negative staphylococci (CNS) isolates were resistant to tetracycline and clindamycin. Overall the proportion of Enterobacteriaceae isolates resistant to at least one antibiotic agents was high (55% of isolates), whereas only 3% benzylpenicillin resistant streptococci were detected. Associations were detected between antimicrobial resistance and particular species of Enterobacteriaceae, CNS and specific S. aureus spa types. In conclusion we present in this study data on causative udder pathogen species and their antimicrobial resistance, which are of great importance for mastitis management and prevention.