Brucellosis, caused by Brucella abortus is a major disease of cattle and a zoonosis. In order to estimate the bovine brucellosis prevalence in Costa Rica (CR), a total 765 herds (13078 bovines) from six regions of CR were randomly sampled during 2012-2013. A non-random sample of 7907 herds (532199 bovines) of the six regions, arriving for diagnoses during 2014-2016 to the Costa Rican Animal Health Service was also studied. The prevalence estimated by Rose Bengal test (RBT) ranged from 10.5%-11.4%; alternatively, the prevalence estimated by testing the RBT positives in iELISA, ranged from 4.1%-6.0%, respectively. However, cattle in CR are not vaccinated with B. abortus S19 but with RB51 (vaccination coverage close to 11%), and under these conditions the RBT displays 99% specificity and 99% sensitivity. Therefore, the RBT herd depicted in the random analysis stands as a feasible assessment and then, the recommended value in case of planning an eradication program in CR. Studies of three decades reveled that bovine brucellosis prevalence has increased in CR. B. abortus was identified by biochemical and molecular studies as the etiological agent of bovine brucellosis. Multiple locus variable-number tandem repeat analysis-16 revealed four B. abortus clusters. Cluster one and three are intertwined with isolates from other countries, while clusters two and four have only representatives from CR. Cluster one is widely distributed in all regions of the country and may be the primary B. abortus source. The other clusters seem to be restricted to specific areas in CR. The implications of our findings, in relation to the control of the disease in CR, are critically discussed.