The isolate 81278ZB15 is a fertile strain of predominant virulence of Magnaporthe grisea in Fujian province, China. Its rep-PCR (repetitive element-based polymerase chain reaction) DNA fingerprint and virulence spectrum are different from those of GUY11, a hermophrodite. Ascospores of the cross 81278ZB15 and GUY11 were randomly isolated and their virulence was tested on CO39 NILs (near isogenic lines, C101LAC Pi-1, C101A51 Pi-2, C104PKT Pi-3, C101PKT Pi-4a, C105TTP-4L-23 Pi-4b and CO39). The results showed that 81278ZB15 has Avr-Pil, Avr-Pi2, Avr-Pi4a and Avr-Pi4b genes. The segregation of avirulence and virulence on Pi-1, Pi-2, Pi-4a in the progeny fits 1:1, but there were 8 recombinant ascospore progeny in these three avirulence loci. The results suggest that Avr-Pil, Avr-Pi2 and Avr-Pi4a in 81278ZB15 are three tightly linked but independent loci. A 1.2 kb DNA fragment based on rep-PCR fingerprint (RPF1.2) was found to link to these avirulence loci. The genetic distance between RPF1.2 and Avr-Pil, Avr-Pi2, and Avr-Pi4a is estimated to be 5.9 cM, 2.2 cM and 2.2 cM respectively. Furthermore, some progenies are avirulent on Pi-3, CO39 and 8 prognies are virulent on Pi-4b although both parents are virulent on Pi-3, CO39 and avirulent on Pi-4b. The possible causes of irregular recombination were also discussed.