From September 2016 to August 2017, four hundred and twenty four milk samples were collected from mammary halves of 212 apparently healthy lactating animals (108 ewes and 104 does) from small private flocks in different localities at Sharkia Governorate. All samples were investigated by California mastitis test (CMT) and bacteriological examination to determine prevalence and etiology of subclinical mastitis (SCM) in sheep and goats and to estimate the mean somatic cell count (SCC) of infected milk samples with different pathogens. The prevalence rates of SCM using CMT were 44 (40.7%) in ewes [59 milk samples, (27.3%)] and 50 (48.1%) in does [62 milk samples, (29.8%)]. Furthermore, out of ewes' and does' milk samples examined by bacteriological culture 54 (25.0%) and 56 (26.9%) samples were bacteriologically positive, respectively. The isolated bacterial causing SCM in ewes' milk samples were E. coli (44.4%), S. aureus (38.9%), Streptococcus spp. (27.8%), coagulase negative Staphylococci (26.0%), Citrobacter spp. (3.7%) and Enterobacter spp. (1.9%). The identified isolates from does' milk samples were S. aureus (46.4%), E. coli (26.8%), Streptococcus spp. (25.0%), coagulase negative Staphylococci (19.6%), Citrobacter spp. (5.4%) and Enterobacter spp. (3.6%). The geometric mean of SCC of milk samples harbored major pathogens was significantly (P < 0.05) higher than those harbored minor pathogens. Polymerase Chain Reaction (PCR) was applied on a total of 26 isolates from the most recovered species associated with mastitic milk samples of ewes and does. Suspected S. aureus, E. coli, Strep. agalactiae, Strep. dysagalactiae, and Strep. uberis isolates showed characteristic bands at 270 bp, 366 bp, 487 bp, 279 bp, and 723 bp which were specific for the used genes, respectively. In conclusion: a great attention should be directed to the early diagnosis of SCM in ewes and does.