We investigated the molecular basis of an extremely late bolting, non-heading 'Leafy Green Parental Line No. 2 (Tsukena No. 2)', to obtain suitable DNA markers for breeding the late bolting trait in Chinese cabbage (Brassica rapa L. ssp. pekinensis). We found that Tsukena No. 2 contains a similar to 5 kbp large insertion near the 5' end of the first intron of BrFLC2, BrFLC3 and BrFLC3', which are homologs of an Arabidopsis repressor gene for floral transition, FLOWERING LOCUS C (FLC). The transcript abundance of BrFLC1 in Tsukena No. 2 was repressed during cold exposure to the same level as found in a mid-season bolting commercial F-1 variety "Muso" (heading Chinese cabbage) and an early-bolting parent of commercial F-1 varieties, "Early" (Sakata Co.), whereas repression of BrFLC2 and BrFLC3 containing the large insertion was weak. Furthermore, QTL analysis of a F-2 population derived from the Tsukena No. 2 9 "Early" revealed that polymorphisms at the BrFLC2 and BrFLC3 loci explained 46.0 and 9.9 % of the phenotypic variation in the bolting time of vernalized plants, respectively. In Arabidopsis, cold-induced repression of FLC and maintenance of that repression are associated with the first intron of FLC. Our study suggests that a naturally occurring large insertion in the first intron resulted in weak repression of BrFLC2 and BrFLC3 during cold exposure and therefore explains the extremely late bolting of the Tsukena No. 2 cultivar.