Marker-assisted selection (MAS) is an important modern breeding technique, but it has been found that the effect of the markers for quantitative trait loci (QTL) is inconsistent, leading in some cases to MAS failure and raising doubts about its effectiveness. Here the model organism Drosophila melanogaster was employed to study whether an effective marker could be found and applied to MAS. We crossed the stock carrying the y (0) marker (a recessive mutation allele of the yellow gene on the X chromosome) with three other stocks carrying corresponding wild-type markers in an F2 design, and found that the y (0) marker was in significant association with low body weight (P < 0.001). This association was consistent across different backgrounds and the marker effects in female and male were approximately 0.95 sigma (P) (phenotypic standard deviation) and 0.68 sigma (P), respectively. We next introgressed a fragment via the y (0) marker into a wild stock background over 20 generations of marker-assisted introgression (MAI), and constructed the introgression stock y (0)(OR)20 in which body weight decreased by 13% and 7%, in female and male, respectively, compared to the wild stock (P < 0.0001). This indicated that there must be a single QTL for low body weight that is tightly linked to the y (0) marker. We then shortened the introgressed fragment to less than 1.5 cM by a deeper MAI using the y (0) marker and the white marker. This narrower fragment also resulted in a similar decrease in body weight to that induced by y (0)(OR)20, indicating that the QTL for low body weight is located within this less-than-1.5 cM interval. Molecular characteristics of the y (0) marker by PCR amplification and Southern blotting revealed that yellow gene was deficient in the y (0) stock, leading to disappearance of melanin from the cuticle and probably influencing the developmental process. The above results confirmed the existence of effective QTL markers applicable to MAS breeding schemes, and their potential application in breeding new stocks.