In this species differentiation study of Corynebacterium spp. (C. spp.), quarter foremilk samples from 48 farms were included. These were obtained from both clinically healthy cows and those with clinical mastitis. First, all samples were examined cyto-microbiologically and all catalase-positive rods were differentiated using the direct transfer method in MALDI-TOF MS. C. bovis, C. amycolatum, C. xerosis, and five other species were identified with proportions of 90.1%, 7.7%, and 0.8% for the named species, respectively, and 1.4% for the remaining unnamed species. In addition, somatic cell count (SCC) was determined by flow cytometry. Based on this, the isolates were classified into four udder health groups: “latent infection”, “subclinical mastitis”, “clinical mastitis” and “others”. Approximately 90% of isolates of C. bovis and C. amycolatum were from latently and subclinically infected quarters. Of the C. bovis isolates, 5.8% were obtained from milk samples from clinical mastitis, whereas C. amycolatum was not present in clinical mastitis. The distribution of groups in these two species differed significantly. The geometric mean SCC of all species combined was 76,000 SCC/mL, almost the same as the SCC of C. bovis. With 50,000 SCC/mL, the SCC of C. amycolatum was slightly below the SCC of C. bovis. Through the species-level detection and consideration of SCC performed here, it is apparent that individual species differ in terms of their pathogenicity. Overall, their classification as minor pathogens with an SCC increase is confirmed.