Subclinical mastitis is well known to cause huge economic losses in the dairy production. In the Afar region of Ethiopia goats are among the most important animals used for milk and meat production. The present study was conducted from February to June, 2014 to estimate prevalence of subclinical mastitis in goats using California Mastitis Test (CMT), to isolate major bacterial pathogens causing mastitis and to establish antimicrobial sensitivity for bacterial isolates. A total of 228 lactating goats from Aba'lla district, Afar region were examined. The prevalence of subclinical mastitis was 20.6% (47/228). Age showed statistically significant association with the prevalence of subclinical mastitis (p = 0.009). However, parity number and length of lactation did not show statistically significant relation with the prevalence of subclinical mastitis in goats. Through bacteriological examinations six different isolates from the CMT positive milk samples were S. aureus (11/47, 23.4%), E. coli (10/47, 21.3%), Streptococcus (9/47, 19.1%), Salmonella (8/47, 17.0%), Staphylococcus (5/47, 10.6%) and others (4/47, 8.5%). Antibiotic susceptibility of the selected isolates was investigated by disk diffusion method. High resistance of Staphylococcus species to penicillin G followed by ampicillin was observed. Streptococci were highly resistant to ampicillin, norfloxacin, ciprofloxacin and clindamycin. E. coli were resistant to clindamycin, whereas salmonella were found to be highly resistant to kanamycin, ampicillin and erythromycin. Some of the organisms were found to be multidrug resistant.