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The Present investigations were carried out to evaluate the resistance levels of Rhyzopertha dominica (F) populations which were collected from six states viz., Uttar Pradesh, Haryana, Punjab, Rajasthan, Madhya Pradesh and Delhi from Food Corporation of India (FCI) godowns. The toxicological experiment was done to investigate, evaluate and understand the levels of resistance in all the populations towards the phosphine. The Phosphine bioassays were done according to the FAO standard bioassay procedure. Two discriminating doses, 0.03 mg/l, and 0.25 mg/l were used to screen the populations for resistance to phosphine. The resistance percentage indicated the tolerance levels of the different populations to phosphine. Dose-response assays were done with different concentrations of phosphine to estimate the median lethal dose values for all the collected populations and evaluated the level of tolerance presented in these populations. The Molecular screening of phosphine resistance was carried out using the CAPS marker and the resistance allele frequency was estimated for all the eighteen populations. The alleles typing for population variation and phylogeographic studies of R. dominica also done in this study.