Coccidiosis continues to be one of the most important issues in animal health and generates significant economic losses to the livestock industry in Indonesia, specifically due to Eimeria spp. Infections. Eimeria are specific to a particular host Eimeria and multi-species infections are more prevalent than infections with only one species. Eimeria zuernii is one of the highly pathogenic coccidia that is a major cause of clinical eimeriosis in livestock. This study's objective was to identify E. zuernii infections in Malang, East Java, Indonesian farms. The oocysts were concentrated and purified using a fecal harvesting method. The genomic DNA is extracted according to the instructions included with the kit. Internal transcribed spacer-1 (ITS1) nested polymerase chain reaction (nPCR) was used to analyze a total of 102 stool samples. Primer pairs specific to E. zuernii, as well as a standard optimum annealing temperature of 55 °C for the species, were discovered. The samples were amplified DNA approximately 334 bp. The results indicated that the prevalence of Eimeria spp. Was57.8% (59/102) by floatation method and specific species, E. zuernii was 35.3% (36/102) by nPCR of cattle fecal samples in Malang, East Java. When Eimeria species are available, the parasite spreads widely through the group inside a couple of life cycles. A pathogenic Eimeria species can infect cattle, thus species identification is critical. Low-infective portions of highly pathogenic species can cause illness, and the productive idea of the parasite quickly prompts high re-contamination. To increase cattle production, eimeriosis management should be considered.