Introduction Staphylococci are the most prevalent bacteria in milk samples collected aseptically from small ruminants. We have determined their prevalence and pathogenicity in sheep and goat milk and characterized the isolates with MALDI-TOF MS, by measuring milk amyloid A (MAA, only in ewe's milk) and haptoglobin (only in goat's milk) and by testing antimicrobial susceptibility. Material and Methods Milk samples were aseptically collected from five dairy sheep and five dairy goat farms in Austria. We also included 54 milk samples from sheep and 6 milk samples from goats that had been sent for analysis to the University Clinic for Ruminants in Vienna (Austria). We used MALDI-TOF MS to confirm all isolates and to differentiate them to the species level. Isolates identified with a MALDI score of between 1.99 and 1.70 (unreliable species identification, reliable genus identification) were further tested with a VITEK (R) 2 system. Milk amyloid A (MAA) in sheep milk samples and haptoglobin (HP) in goat's milk were analysed to estimate the pathogenicity. Antimicrobial susceptibility testing was performed with a microdilution test and somatic cell count was measured with the DCC (R) cell counter, a portable device for on-farm SCC analysis in milk. Results Of the 1510 half-milk samples analysed, 81.3 % (n = 1227) were negative in the bacteriological examination. Non-aureus-staphylococci (NAS) were isolated from 16.0 % (n = 242) and Staphylococcus (S.) aureus from 1.3 % (n = 19) of the samples. A total of 66.0 % of the isolates (n = 163, including all S. aureus) were identified with high reliability (MALDI score > 1.999) at the species level. There were significant differences between S. aureus and NAS in terms of somatic cell count (SCC, p<0.001) and the acute phase protein haptoglobin (p<0.001, only analysed in goat milk). Milk SCC (p=0,001) and MAA (p=0,030) content varied significantly in milk samples with different NAS-species, while the effect of NAS-species on milk HP was not significant (p=0,280). Pairwise comparisons (n = 179, milk of sheep and goats) revealed significant differences of SCC in milk samples with detection of S. auricularis and S. simulans (p=0,010) and in milk samples positive for S. auricularis and S. epidermidis (p=0,021). Only one S. aureus isolate but 17 % of the NAS were resistant to penicillin. The rates of resistance to erythromycin were 24.0 % for NAS and 15.8 % for S. aureus. Conclusion MALDI-TOF MS is suitable to identify a wide range of mastitis-relevant staphylococci isolated from sheep and goat milk to the species level. To broaden the level of identification it will be necessary to include further NAS spectra in the MALDI-TOF MS database.