Molecular marker-based selection in plant breeding requires not only suitable molecular markers closely linked to the known genes, but a simple, economic and reliable analyzing technique. We report here a useful PCR marker for genetic diagnostics in breeding for resistance to rice bacterial blight. Xa21 is a newly found gene of rice which confers resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae. We produced two F2 populations between one resistant line IRBB21 containing Xa21 and two susceptible varieties, respectively. One PCR marker, PB78, detected polymorphism between the susceptible varieties and the resistant line. Cosegregation between Xa21 and PB78 was studied in the two F2 populations. The results showed that Xa21 was closely linked to the molecular marker, the crossing over value was 2.48%. Marker-based selection revealed that 100% of the plants with homozygous resistant genotype of PB78 showed resistance to bacterial blight. The available approaches detecting molecular markers in plant breeding are also discussed.