We had developed genome-wide 84634 ISM and 16510 InDel-fragment length polymorphism-based ILP markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17-79%) and well-defined precise admixed domestication pattern was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9-21.6% PVE) were mapped on five rice chromosomes of a high- density genetic linkage map (IR64 x Sonasal) (inter-marker distance: 0.98 cM) anchored with 2785 known cloned/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through this user-friendly web-resource, “Oryza ISM-ILP” marker database. The known/cloned and candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally-relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice.