Lutein is the most abundant plant carotenoid that plays a role in retina protection against photo-stress. The aim of this study was to develop lutein or zeaxanthin specific gene markers from rice which, will be used in breeding program for developing high lutein or zeaxanthin varieties. Lutein content was examined by High Performance Liquid Chromatography. The result showed that Kum Noi, black pericarp rice, had the highest lutein content and was used as donor parent for F1, F2, BC1F1, BC1F2 และ BC2F1 populations production. Carotenoid biosynthesis gene sequence and expression level from different pericarp color rice were analyzed by transcriptome and whole genome sequencing using for gene specific marker development. Fifteen of gene specific markers were designed which were 11 genes of carotenoid synthesis pathway (PSY1 /crtB; phytoene synthase, PDS; phytoenede saturase, ZISO; ?-carotene isomerase, ZDS ; ?-carotene desaturase, CrtISO; carotenoid isomerase, lcyE; lycopene ?-cyclase, lcyB; lycopene ?-cyclase, CYP97A3 /LUT5; cytochrome P450-type hydroxylase A3, CYP97C/ Lut1; cytochrome P450 carotene epsilon-hydroxylase , CYP97B2; cytochrome P450 B and OsEHY /HYD3; ? -carotene hydroxylase), 1 histone modification gene (SDG8; histone methyltransferase), 1 bHLH transcriptional factor gene (bHLH_B2_Kala4) and 2 of cleavage genes (LCD_CCD1; lycopene cleave dioxygenase and NCED2;9-cis-epoxycarotenoid dioxygenase 2/ CCD4b; carotenoid-cleavage dioxygenase 4b/Zeaxanthin cleavage oxygenase). Then simple regression analysis revealed that B2_Kala4 showed association with lutein content (17.13%) and no marker was associated with zeaxanthin content. Moreover, these gene specific markers will be used in molecular marker assisted selection for high lutein breeding.