Abstract: The disclosure discloses a method and application for rapid and accurate chromosomal location of economic traits in laver, belonging to the fields of genomics and molecular breeding, wherein comprising the following steps: distinguishing the different genotype sectors by the color difference of pigment mutants, releasing monospores based on the asexual reproduction of single-genotype sectors, forming offspring CMD population; performing QTL-seq analysis on the extreme phenotype pools of offspring CMD population by SNP/InDel markers; and combining KASP and RNA-seq to predict the location of the genes of discrete traits or major QTL. The disclosure may solve the problem of difficulty in genetic analysis of various traits caused by the genotypic chimeric haploid characteristics.