Coccidiosis caused by Eimeria species is a major form of intestinal infection affecting intensively and semi-intensively reared goats. The province of Alentejo is the main goat-producing area in Portugal. Therefore, all 15 Serpentina goat farms in Alentejo were analyzed regarding the occurrence and diversity of Eimeria species. Fecal samples obtained from 144 animals (52.1% dairy goats, 47.9% pre-pubertal goats) were examined using the modified McMaster technique to determine the number of oocysts per gram of feces. Eimeria spp. oocysts were present in 98.61% of the fecal samples and, overall, nine different Eimeria species were identified. The most prevalent species were E. ninakohlyakimovae (88%) and E. arloingi (85%), followed by E. alijevi (63%) and E. caprovina (63%). The average number of oocysts shed was significantly lower in dairy goats than in pre-adult animals. Astonishingly, no clinical signs of coccidiosis were observed in any of the animals examined, even though they were shedding high numbers of oocysts and were infected with highly pathogenic species. Thus, implementation of routine diagnostic investigation of the occurrence and diversity of caprine Eimeria species may be a useful tool for determination and better understanding of their potential economic impact on goat herds in southern Portugal.