In order to analyse genetic relationships between functional strain Xhhh previously constructed through protoplast fusion for pharmaceutical wastewater treatment and its parents, random amplification polymorphic DNA (RAPD) and polymerase chain reaction (PCR) were used to investigate genetic similarities among the strains based on genome and functional genes analyses. A total of 739 clear and consistent bands were produced in the RAPD fingerprint analysis with 40 primers. The genetic similarity indices between Xhhh and parental strains PC (Phanerochaete chrysosporium), SC (Saccharomyces cerevisiae) and XZ (native bacterium Bacillus sp.) were 36.21%, 37.73% and 37.48%, respectively. With PCR amplification and DNA sequencing, Xhhh was found containing functional genes of mnp and lip from PC, FLO1 from SC and 16S rDNA fragments from XZ. Experimental results of genetic analyses were in accordance with Xhhh biochemical and phenotypic characteristics, and protoplast fusion technique is considered as a promising technique in environmental pollution control.