To provide methods of creating trait prediction models for predicting phenotypes of traits from single nucleotide polymorphism data and methods of predicting traits with which traits can be predicted with a high accuracy. This is a method of creating a trait prediction model for predicting a phenotype of a multifactorial trait using data of a plurality of single nucleotide polymorphisms linked to a trait for each of a plurality of individuals of an organism: representing each of the plurality of single nucleotide polymorphisms as a matrix; classifying the plurality of single nucleotide polymorphisms into a plurality of categories based on their genetic architectures; calculating, for each of the categories, a genomic similarity matrix using the represented matrix and the number of the single nucleotide polymorphisms belonging to the category; and applying the genomic similarity matrix and a parameter of the genetic architecture to a linear mixed model.
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