Abstract: SARII-628 is one of the natural twin-seedling populations, which are maintained in Rice Institution of Sichuan Agricultural University. Haploid-diploid (n: 2n) twin-seedlings can annually emerge from SARII-628. In this study, cDNA-AFLP technique was applied for these haploid and diploid plants. The double stranded cDNA were synthesized from the total RNAs of the roots, stems, panicles, and leaves of three haploid and one diploid plants. Then, EcoRI/MspI combina-tion was chosen for expression difference analysis with cDNA-AFLP technique among the 16 samples. Thirty pairs of primers were selected to amplify 633 loci. Among them, 49 loci were differently expressed. As shown by cDNA-AFLP, the expression levels of haploids were different among individuals but not significant. The average ratio of sensitive loci (acti-vated loci + silenced loci) in haploids was 5.14%, which was higher than that of diploid (3.93%). According to the presence or absence of the bands in root, stem, panicle, and leaf, out of the 14 types of amplified patterns, only 4 exclusively oc-curred in haploid and the corresponding loci were thus haploid-specific in expression. The collecting analysis for the si-lenced and activated loci among different organs of the three haploids revealed that the silenced loci were more than the activated ones in roots and panicles. An opposite trend was observed in panicles and leaves. However, the total number of the activated loci in all the four types of haploid organs was more than that of the silenced loci. The number of sensitive loci is the highest in root, while that in panicle is the least, which suggested that gene expressions were organ-specific.