Chalkiness is a major constraint on rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. In this study, we conducted grain chalkiness gene identification using co-dominant insertion/deletion (INDEL) markers and SSR marker combination on 50 different varieties. The application results in 7 InDel markers and SSR marker on chromosome 7 were recorded. Three primers, InDel 5, InDel 14 and RM21938, associated with grain chalkiness. For the InDel 5 primer, the amplification product was 100%. Use of primer InDel 5 in detection and evaluation of genotype to the chalkiness trait of rice grain on 50 rice varieties indicated the suitability level with phenotypic evaluation was 86% and the unsuitability level was 14%. For the InDel 14 primer, the amplification products were 100%. The suitability with phenotypic assessment was 84% and the unsuitability was 16%. For the RM21938 primer, the amplification product was 94%. The suitability with phenotypic assessment was 76% and the unsuitability was 24%. Thirteen of the selected varieties had grain chalkiness gene both InDel 5, InDel 14 and RM21938. Total 13 varieties were detected from InDel 5, InDel 14 and RM12938 primer combinations also showed high efficiency of the InDel technique in identifying chalkiness gene in rice grain. A cluster analysis was performed and a dendrogram was constructed which evinced the nature of phylogenetic classification among the genotypes of the varieties. These markers could be used for developing quality of rice in breeding program.