Identification and selection for P-deficiency tolerance genotypes of rice-based on phenotypic performance alone are less reliable and might delay progress in breeding works for sustainability. The recent advent of molecular markers or simple sequence repeats (SSRs) can be used to identify P-deficiency tolerant rice genotypes. The current study aimed to assess and confirm phenotypic and genotypic variations in P-deficient tolerance in the selected susceptible and tolerant North Korean indigenous rice varieties (including the control) in order to exploit and display trait ability to low-P tolerance in hydroponic rice improvement. It is equally intended to standardize an efficient and effective protocol for identification and selection of tolerant genes using GWAS (Genome Wide Association Studies) which are hypothesis free methods for identifying associations between genetic regions (loci) and traits for proper growth and regeneration genotype under hydroponic culture for low P. 23 genotypes of North Korean rice were selected based on P deficiency tolerance and grown in the green house under hydroponics for 5weeks and traits such as Tiller Number (TN), Plant Height (PH) Root Length (RL), Shoot Length (SL), Root Dry Weight (RDW), Shoot Dry Weight (SDW) and Plant Weight (PW) were recorded. Two treatment levels of phosphorus that is 10 ppm and 1ppm for normal and P-deficient conditions respectively were introduced every week into hydroponics medium including the addition of other macro and micro nutrients in the solutions. The pH was maintained at 5.5 every week. Experiments were arranged in a randomized complete block designs with 3 replications. Leaf samples of these rice genotypes were equally taken for DNA extraction and the quantitative trait loci that confers P deficiency in some North Korean rice genotypes was identified as Pup1 (using pup 1 markers) that helps rice increase P uptake. GWAS was also used to identify and select candidate genes responsible for low P tolerance.