The present study was conducted in Sheikhupura and Kasur districts for molecular based confirmation of B. abortus in both sheep and goats. Brucellosis in sheep and goats is caused by B. ovis and B. melitensis, respectively but B. abortus (causative agent of bovine) may cross the species barrier to infect the small ruminants which may complicate the control measures of brucellosis because most of the control programs rely on serological screening of brucellosis rather than molecular assay which could confirm the particular species circulating in ruminants. In this study 960 and 471 serum samples of goats and sheep were collected, respectively. After screening with Rose Bengal test (RBT), all seropositive samples were subjected to real-time PCR assay. RBT confirmed the seroprevalences of 19.32% ± 0.289 and 12.29% ± 0.0105 brucellosis in sheep and goats, respectively and real-time PCR confirmed the B. abortus in 74 samples (62.71% ± 0.044) out of 118 seropositive samples in goats while 63 samples (69.23% ± 0.048) out of 91 seropositive samples of sheep. The presence of B. abortus in small ruminants could be due to mixed farming of small and large ruminants, sharing of same pasture, presence of reservoirs host in a farm, which might be the main risk factors for cross-infection of Brucella species in their non-specific hosts. B. abortus could be identified as causative agent of caprine and ovine brucellosis in Pakistan. Results of this study can be used for the development of effective eradication and control strategies for brucellosis in small ruminants.