Linkage maps have been developed for bulb onion (Allium cepa L.) and bunching onion (A. fistulosum L.). It is considered that a high level of macrosynteny exists between these 2 species since they belong to the section Cepa and have the same chromosome number (2n=16). However, a detailed comparison has not been evaluated because there are few common markers onto the maps of both species. The objective of this study was to evaluate synteny at the genome-wide level between bunching onion and bulb onion. As a first step, we developed a basal linkage map in F2 population between yellow bulb onion and red shallot. Since bulb pigmentation and anther color were segregated at 3:1 ratio in F2, we also scored and defined Pg and Ant1 as trait markers, respectively. In addition, F2:3 lines were investigated for the degree of bulb pigmentation. Two SNP markers of candidate genes involved in the flavonoid biosynthesis pathway, flavonoid 3'-hydroxylase (F3'H) and dihydroflavonol 4-reductase (DFR), were also investigated genotypes for F 2 individuals. Linkage map consists of 11 linkage groups with 164 markers covering 1,040 cM. Although both SNP markers (F3'H and DFR) were located on the Chr. 7, two trait markers, Pg and Ant1, were closely linked to DFR. A QTL for bulb pigmentation was also detected on the Chr. 7. All individuals homozygous for onion allele at DFR loci showed no pigmentation in F2 individuals. The degree of red pigmentation became significantly darkened by replacing shallot allele at DFR in both F2 and F2:3. Therefore, DFR is one of key genes involved in bulb color in this population.