In the course of quantitative trait loci (QTL) analysis of the back cross (BC1) families of olive flounder (Paralichtys olivaceus), we observed significant segregation distortion at a microsatellite marker Poli9-58TUF in two crosses of informative progenies. The family 1 of the random BC1 progenies derived from a cross between a F1 male genotype (A/B) and a F1's female parent genotype (A/C) and the family 2 (A/C x A/C) displayed a strong bias in the locus from the Mendelian inheritance by the elimination of homozygous A/A genotype. The deleterious roles of the AA genotypes are suggested during the metamorphosis and it implies that the parents of these families carried a recessive gene or genes hampering development at an early stage because the offspring of the double heterozygote parents show the reduction in frequency or elimination of one homozygous class, which is an evidence for linkage between the genetic marker and gene(s) with recessive deleterious alleles. This data support a hypothesis that the region contains a recessive lethal gene or genes.