The present invention provides a novel polymorphism detecting method suitable for the detection and identification of copy number variation.Provided is a method of determining the genotype of a subject in a genomic region comprising an SNP site, comprising a step for performing typing of the SNP site by the invader assay with a DNA-containing sample comprising the genomic region from the subject as the template, wherein fluorescence is measured on a real time basis. The copy number ratio of both alleles is determined using the fluorescence intensity ratio of each allele at a time before saturation of fluorescence intensity. Preferably, the present method further comprises a step for amplifying the genomic region comprising an SNP site prior to the invader step. In this step of amplification, a plurality of regions comprising a plurality of SNP sites can be simultaneously amplified. Furthermore, the present method enables the determination of the copy number of each allele when combined with quantitative PCR.