Introgresion is a term used to describe the infiltration of genes from one species into the gene pool of another species, generally referring to the incorporation of genes from one species into another.When the parents are known, the similarity between the genotypes of the parents and the samples can be compared to determine which fragments may infiltrate into the samples from the parents.However, for known gene penetration in two populations, parental locations, it is not possible to predict introgression fragments by comparing direct samples. This method is used to predict which fragments of sample X in population A may be infiltrated from population B by judging the genotype similarity of population A and B, and vice versa.For example, the existing 200 sea island cotton and upland cotton material, have been completed sequencing, and in upland cotton VCF file reference genome for SNP set, this method can predict each material in upland cotton, whether there is came from sea island cotton group gene fragments, in this case, we called the upland cotton group testing group, group of sea island cotton is called source. The idea of this method is to take the population genotype as a reference. If the similarity between a segment of a material in the test population and the genotype of the source population is much greater than that between it and the genotype of the test population, then we can assume that the segment is infiltrated from the source population.