The rice cultivars Ningnong black carp and high indica rice exhibited low and high content on γ-aminobutyric acid, respectively. Both genotypes were deployed for generating a F2 population that comprises of 216 individual plants. By taking use of 130 polymorphic SSR markers, a linkage map was produced with an length of 2406.9 cM. Each linkage group expands from 129.5 to 360.7 cM, and a mean distance between markers was 18.5 cM. The QTL mapping positioning study showed that seven QTL loci controlling the γ-aminobutyric acid content were found on chromosomes 8 and 9, respectively. The contribution rate of qGABA8-2, qGABA8-3, qGABA9-1 was 10%, 11% and 9%, respectively. The composite interval mapping was performed on three QTL sites with large contribution rate. When LRS was 25.6, a QTL qGABA8 was initially found at RM342-RM515 in an interval of 326Kb. The confidence interval was further delimited to 180 kb by using the InDel marker G121. Therefore, the accumulated results of this study might be useful in further gene isolation and marker-assisted screening for the genotypes with the enriched amino butyric acid.