There were 6 target DNA fragments of the three parental strains existing in the cell of genetically engineered microorganism strain (GEMs) Fhhh measured in this research by polymerase chain reaction (PCR). And Fhhh was a fusant GEMs of the three parental strains Phanerochaete chrysosporium; Saccharomyces cerevisiae and the native bacterium YZ1, and they have the 6 target DNA fragments of mnp1, mnp2、lip1、lip2,FLO1 and 16SrDNA respectively. The results showed that Fhhh contained the total 6 target DNA fragments with the molecular genetic stability. Meanwhile the PCR productions of the three parental strains only had their target DNA fragments individually and were different from each other. It may illustrate that the technique of the inter-kingdom protoplast fusion through the process of intercellular gene recombination can be used as a reliable bioengineering technique to construct the specific stain for the pollution control.