Random amplified polymorphic DNA (RAPD technique) gives characteristic fingerprints or genetic polymorphism for Eimeria stiedae isolates. The isolates were collected from three different localities in Egypt (Al-Bahyra, Assiut and El-Kalybia provices). Four oligonucleotides primers reflected different phylogenetic relationship among the 3 Eimeria stiedae isolates. The degree of similarity between the 3 isolates reflected the presence of both species specific and even strain-specific band, the statistical analysis suggested a closer phylogenetic relationship between Al-Bahyra and Assiut Eimeria stiedae isolates which are distantly related to El-Kalybia isolates RAPD technique could easily differentiate with a great potential the minor changes in the genomes of the related genotypes of Eimeria stiedae isolates in Egypt.