The dairy goat industry is rapidly developing worldwide as a result of increasing the awareness about the high quality and nutritional properties of caprine milk. Subclinical mastitis (SCM) is one of the most important challenges facing goat industry and leading to great economic losses. S. aureus has been regarded for long time as one of the most leading cause of mastitis either clinical or subclinical. The present study aimed to investigate the prevalence of SCM among goats and to isolate S. aureus as well as study some of their phenotypic and genotypic characters. A total of 143 individual half milk samples (HMSs) were collected aseptically from 75 apparently healthy goats and examined. S. aureus were isolated and identified phenotypically using conventional methods in addition to using Vitek2 compact system. The selected isolates were confirmed by the detection of staphylococcal 16S rRNA gene. The prevalence of SCM based on California Mastitis Test (CMT) was 41.3 and 34.3% at goats and udder HMSs levels, respectively. The prevalence of S. aureus isolation in subclinically mastitic goats was investigated in 49 HMSs as 26.5%. The results of in-vitro antimicrobial susceptibility of S. aureus isolates against 12 antimicrobial agents showed high resistance against ampicillin, amoxicillin-clavulanic, cefoxitin, cefotaxime and vancomycin. Meanwhile, high susceptibilities were recorded against ciprofloxacin, levofloxacin, florophenicol, doxycycline HCl, clindamycin, gentamicin and sulfamethoxazole-trimethoprim. The haemolytic activity and biofilm formation on CRA medium were investigated in all isolates. The haemolytic activity was detected in 76.9% of isolates meanwhile 53.8% of isolates were biofilm formers, respectively. The results of genotypic detection of mecA, blaZ and vanA resistance genes using PCR showed that they were detected in 100, 71.4 and 42.9% of the tested isolates, respectively. Meanwhile, biofilm and α-haemolysin coding genes (icaD and hla) were detected in 71.4 and 42.9% of the tested isolates, respectively. It was concluded that S. aureus is one of the most prevalent cause of caprine SCM and the existence of high percentages of antimicrobials resistance as well as resistance and virulence genes represent risk factors and public health hazards and possible danger of lateral transfer of resistance genes to other microorganisms in both animals and humans.