Eight Japanese bunching onion (Allium fistulosum L.)-shallot (Allium cepa L. Aggregatum group) monosomic addition lines (MALs, FF + 1A-FF + 8A) were used to reveal the effects of single alien chromosomes of A. cepa on the production of amino acids and S-alk(en)yl-L-cysteine sulfoxides (ACSOs) in leaf tissues of A. fistulosum. Amino acid and ACSO contents in MAL leaf blades were determined once every 3 months from August 2005 to May 2006. The amino acid found in the greatest amount in all of the MALs throughout the year was cysteine, except for FF + 7A accumulated glycine as the greatest amount of amino acid (Nov. 2005). All of the MALs contained three ACSOs in varying amounts and proportions, and all accumulated S-1-propenyl CSO as a major ACSO but hardly produced S-2-propenyl CSO throughout the year. FF + 3A showed greatly increased proportions of Smethyl CSO in total ACSO, suggesting that anonymous genes controlling S-methyl CSO production are located on chromosome 3A of shallot. High accumulation of total ACSOs in the monosomic additions FF + 3A, FF + 4A, FF + 5A, and FF + 8A was observed during different growth periods. Using PCR-based marker analysis, sulfate transporter, adenosine 5'-phosphosulfate reductase (APSR), serine acetyltransferase, O-acetylserine thiol-lyase, glutamylcysteine synthase, glutathione synthase, and γ-glutamyl transpeptidase candidate genes related to sulfur assimilation and ACSO biosynthesis were allocated to chromosomes 7A, 2A, 7A, 7A, 2A, 7A, and 4A, respectively. This result showed little association between the chromosomal locations of these genes and ACSO accumulation, suggesting that anonymous genes controlling ACSO accumulation were dispersed on the 2A, 3A, 4A, 5A, 7A, and 8A chromosomes of shallot. APSR gene expression was inhibited by 5A chromosome additions, suggesting that one of the regulatory genes was located on a 5A chromosome and inhibited APSR expression.