Abstract: The differential expression between merozoites of maduramisin sensitive and maduramisin resistant strains of E. tenella was detected with the technique of random mRNA Differential Display. The 34 differential DNA fragments were identified by reverse Northern dot hybridization. Four fragments were found to be really different, the differential expression fragments were cloned into pMD-18T vector and sequenced. Then the possible functions and the relationship of the 4 differential DNA fragments to drug resistance were predicted with Blast. Fragment ACD3-2 was found to be similar to Eimeia tenella microneme-5 gene, which is related to the parasite invasion, moving; Fragment HCD1 similar to part sequence of Eimeia tenella surface antigen-17, 16 genes, the other 2 differential expression sequences maybe new genes because no homologous gene were found in GenBank by Blast analysis.