Understanding the occurrence and distribution of various Eimeria species in broiler farms is necessary to develop effective coccidiosis vaccines. In the current study, fecal samples were collected from broilers with subclinical signs at fifty small-scale farms in the Shandong province in eastern China. Oocysts purified from fecal samples were examined for morphology. The Eimeria genomic DNA extracted from each sample was subjected to PCR amplification with species-specific primers for the internal transcribed spacer sequence or the small RNA subunit sequence of each of the seven species of Eimeria found in chickens. The results showed that more than one Eimeria species existed in most fecal samples, and the infection rate of identified Eimeria spp. in these farms was 90%, 88%, 72%, 68%, 60%, 26%, and 8% for E. tenella, E. praecox, E. acervulina, E. maxima, E. mitis, E. necatrix, and E. brunetti, respectively. This indicates that E. tenella, E. praecox, E. acervulina, E. maxima, and E. mitis are the predominant species in local Shandong province, so an effective coccidiosis vaccine applied in this area should contain at least these five Eimeria species.