While a diploid potato was continuously selfed by a function of Sli gene, the level of heterozygosity reduced, and the fertility also reduced (inbreeding depression), which might be improved because continuous selfing could eliminate undesirable recessive alleles. To explore what was occurring as advancing self-generations in terms of fertility, 51 plants of an S 3 diploid potato family were evaluated for fertility-related traits and analyzed by RFLP markers. The level of heterozygosity was positively correlated with any of fertility-related traits (r = 0.108 − 0.333). At least six loci on six chromosome sections were associated with fertility-related quantitative trait loci (QTLs), of which three performed better in the heterozygotes and three in the homozygotes. By further continued selfing, QTLs performing better in heterozygotes were likely fixed to homozygotes with secondly better performance, and those performing better in homozygotes were fixed to the best genotypes. Thus, the selfed progenies were cryptically being improved for fertility by genetic fixation to the best or better genotypes in fertility-related QTLs.