The amylose content and fragrance in rice are controlled by Wx and fgr respectively. Here, based on the gel-based FMs reported previously, we developed two HRM(high resolution melting)-based FMs Wxa/b and BAD2E7 to study the genotype of 88 rice accessions in Wx and fgr gene. We implemented the LightScanner 96 platform to determine the HRM curves, through which each determination for up to 96 samples could be done in less than 10 min. The result showed that the amylose content of 25 homozygous Wxa accessions and 59 homozygous Wxb accessions was 25.08% and 15.00%, respectively, and that of 4 heterozygous (Wxa/Wxb) accessions was 18.13%. All grains of 3 accessions (Bataixiangzhan, Xiangyaxiangzhan and Basmati 370) harboring homozygous fgr were fragrant, and only partial grains of 2 accessions with heterozygous fgr were fragrant. Thus it can be seen that the HRM-derived functional markers could be applied to rapidly and accurately predict their corresponding phenotypes, showing good application prospects in rice breeding practice.