The aim of this study was to determine the presence of species of the genus Eimeria species in naturally infected bovines in Southern Bahia, Northeast Brazil. The study population comprised 117 Zebu crossbred cattle that belonged to 10 dairy herds with extensive or semi-extensive production systems. The modified Gordon and Whitlock technique was used to determine positive samples and number of oocysts per gram of feces. Statistical analyses were performed using the chi-square test with Yates correction and a 95% confidence interval. Thirty-nine cattle (33.33%) were positive, and ten different species were identified in infected animals: E. bovis (24.79%); E. canadensis (8.55%); E. zuernii (6.83%); E. ellipsoidalis (5.99%); E. cylindrica (3.42%); E. auburnensis (3.42%); E. brasiliensis (2.56%); E. bukidnonensis (1.71%); E. alabamensis (0.85%), and E. subspherica (0.85%). Higher parasitism was observed in animals up to one year of age (p = 0.005), but no animal presented clinical signs of the disease. As the presence of clinical eimeriosis was not evidenced and all animals were Zebu crossbred cattle from extensive or semi-extensive production systems, further studies should be conducted to investigate the effects of these factors on disease development.