Vigorous seedling growth is a desirable trait for machine-assisted transplanting using a plug nursery system in bunching onion. This study was undertaken to identify the quantitative trait loci (QTLs) controlling seedling growth and to elucidate the modes of gene action of the QTLs. Plant material was a set of reciprocally backcrossed populations (BC1). These were produced from 2 inbred lines derived from the Senju group and Kujo group. Two corresponding. BC1 maps were constructed by adding co-dominant simple sequence repeat (SSR) markers to the previously reported amplified fragment length polymorphism (AFLP) based maps. Fresh weights of seedling's were measured in 3 seasons using BC1S1 families. Remarkable heterosis was observed in F, and many BC1S1 families. Many QTLs for seedling weight were detected on the 2 maps by composite interval mapping. The phenotypic variation explained by a single QTL was less than 25%. Of these, 3 QTLs on 3 linkage groups are considered to be consistently effective across different environmental conditions because they were detected in years and seasons. Most QTLs were detected on one map, but were not detected in a corresponding different region on the other map; however, the degree of dominance at each locus was calculated to determine whether the locus shows overdominance. Overdominance was observed at some loci, and the other loci showed an additive and dominant effect. It is suggested that remarkable heterosis for seedling weight in the present population is based on the accumulation of dominant and overdominant gene actions.