In amplifying a region containing two allelic genes, the polymorphism of one of the allelic genes is positioned at or near the 3′ end of an amplification primer, so that the chain would extend only from one of the two primers, one that matches the mutant type nucleotide(s) and one that matches the wild-type nucleotide(s). The other primer is unaffected by the allelic genes but is positioned to include the other allelic gene in the amplicon. The PCR amplifies only the target genomic DNA having one specific allele of the first allelic gene. The technique exploits the fact that the haplotype of the first and the second allelic genes can be determined if the allele of the second allelic gene in the amplicon can be identified. Designing probes with complementary sequences for identifying the two alleles (major and minor) of the second allelic gene, and fixing the probe set on a solid support and hybridizing them with the amplicon to identify the probe that forms a hybrid, are characteristic features of the present invention.