Objective. To clone complete EcoRII restriction endonuclease gene （ecoRIIR） and methyltransferase gene （ecoRIIM） in one vector and to analyze the coordinating expression of this whole R M system.Methods. Unidirectional deletion subclones were constructed with ExoIII.ecoRIIR/M genes were preliminarily located in the cloned fragment according to the enzyme activities of subclones. Exact deletion sites were determined by sequencing

and transcriptional start sites were determined by S1 mapping. Results. The DNA fragment which was cloned into pBluescript SK+contained intact ecoRIIR gene andecoRIIM gene

and two transcriptional start sites of ecoRIIR gene were determined. 132bp to 458bp from 3’end of ecoRIIR gene are indispensable to enzyme activities and deletion of 202bp from 3’end of ecoRIIM gene made enzyme lose the capability in DNA protection to resist specific cut with EcoRII endonuclease （EcoRII.R）. Deletion of the coding and flanking sequences of one gene did not affect the expression of the other gene

and the recombinants only containing ecoRIIR gene appeared to be lethal to dcm+host. Conclusion. ecoRIIM gene linking closely to ecoRIIR gene is very important for the existence of the R M system in process of evolution

but the key tocontrol EcoRII R M order may not exist in transcriptional level .