Brucellosis is a zoonotic infectious disease in western regions of Iran, especially in Hamedan province. Following the Famenin brucellosis cohort study, the main aim of the current study was the molecular detection of Brucella species (spp.) in sheep and goats from Famenin, Hamedan, Iran. A total of 23 Brucella-seropositive samples (sheep=21 and goats=2), which had been screened from 1,660 animals in the Famenin cohort study, were used to detect Brucella-DNA using the BCSP31 target gene and IS711 locus. In total, 20 of 23 samples were positive for Brucella infection by using specific primers. Additionally, Brucella melitensis (B. melitensis) and Brucella abortus (B. abortus) were confirmed in 90% (n=18) and 10% (n=2) of positive samples, respectively. There was no sample with the co-infection of B. abortus and B. melitensis. In this study, B. abortus was isolated from one of the goat samples. This is the first report on Brucella spp. in animals in the region. It was found that B. melitensis is the dominant spp. responsible for brucellosis in animals from Famenin. Molecular techniques are reliable tools to detect Brucella infection, especially in cases without serology findings and conclusive results.