Mastitis is defined as an inflammation of the mammary gland, which widely affects ruminants, such as cows, sheep and goats. Worldly recognized as an indicator of milk quality and udder health, assessment of somatic cell count (SCC) still the gold standard for recognition of subclinical mastitis cases in dairy cows farms. The objective of this work was to describe the relationship between pathogens identified from goat milk by matrix-assisted laser desorption/ ionization-time of flight (MALDI-ToF) and SCC values. Total of 98 aseptic milk samples were collected (15 mL) during morning milking from 47 Toggenburg and 4 Alpine goats at a commercial dairy goat farm in South Dakota. Goats were between 2 and 8 years-old, at the end of lactation stage. To perform the microbiological test, 10 µL of milk were spread onto 5% sheep blood agar and incubated for 24/48 h. The isolates were submitted to MALDI-TOF for species identification and SCC was determined through a service provider (Eurofins DQCI, Mounds View – MN). A total of 74% (n = 73; SCC ranging from 42 to 13,186 × 10³ cells/mL) of all milk samples were bacteriologically negative. Among the positive milk samples, the distribution of bacteria identified and range of SCC were as follows: 42% Staphylococcus simulans (n = 11; 958 to 8,164 × 10³ cells/mL), 15% Staphylococcus aureus (n = 4; 1,828 to 25,392 × 10³ cells/mL), 11.5% Staphylococcus chromogenes (n = 3; 507 to 1,825 × 10³ cells/mL), 11.5% Bacillus spp. (n = 3; 501 to 1,196 × 10³ cells/mL), 8% Staphylococcus epidermidis (n = 2; 1,552 to 3,163 × 10³ cells/mL), 8% Staphylococcus caprae (n = 1; 1,828 × 10³ cells/mL) and 4% Staphylococcus warneri (n = 1; 375 × 10³ cells/mL). Chi-squared test was done and a significant difference was observed when SCC values from positive and negative samples were compared (P < 0.001). However, values of SCC show high variability within and between pathogens. Since non-infectious factors also impact SCC in dairy goats the interpretation of this test requires attention, thus caution should be used when using solely SCC as a diagnostic tool.