Glutinous Bora rice plays an important role in socio-economic and cultural livelihood of Boro tribes of Assam. However, neither systematic survey had been done, nor databanks are available on their detailed morpho-molecular characterization essential for breeding programme. Present study attempts to prepare a morphological database with molecular signature using a total of 22 Bora rice lines collected from upper Brahmaputra basin of Assam, which were phenotyped with 27 popular agro-morphological traits followed by marker based genotyping, sequence diversity study and expression profiling for selected genetic loci associated with low amylose content. Long day flowering and less number of tillers and panicles are the main discouraging traits of Bora rice that showed negative association with tiller length. Among the 8 different phenotypic markers established, anthocyanin pigment in different parts of the plant and availability of awn may be used as identifying criteria for selection of the hybrid lines introgress with “komal” trait. In marker based genotyping, all the studied marker loci were reported to be polymorphic with variable number of allelic forms and RM241 showed highest PIC value. In case of expression study, 5 days (after anthesis) old developing grains of selected Komal genotype (Aghani Bora) showed 90.9-fold down regulation of GBSSI (loci associated with amylose deposition in rice grain) with respect to the commonly grown popular rice (IR36). Phylogenetic relationship study with 5 different genomes (O rufipogon, O glaberima, O sativa japonica group, O sativa Indica group and IR36) based on sequence diversity of six major genetic loci (associated with starch deposition in endosperm) showed distinct relationship. Selected morpho-molecular markers (polymorphic between Bora and normal rice) were subjected to validation on hybrid population developed from selected Bora rice (Vogali Bora) and normal rice (IR36), which showed a promising response for use in marker assisted breeding program.