The relationship of several candidate genes polymorphisms with breeding values of economic traits were investigated in Korean Native Pigs. Record (2001-2006) of 546 Korean native pigs were obtained from National Institute of Animal Science, Korea having data on average daily gain (ADG), age at 70 kg (D70 kg) and backfat thickness (BF). The data's obtained were analyzed by the DF-REML (Derivative-Free Restricted Maximum Likelihood) program of Boldman using a single-trait animal model to analyse the genetic parameters. The analysis of restriction fragment length polymorphism (RFLP) was conducted on 68 Korean native pigs (KNP) using single nucleotide polymorphism (SNP). Different genotype frequencies of 5 candidate genes such as MC4R, PRKAG3, FABP3, ESR and PRLR3 were observed in KNP. Significant relationship of AA and AB genotype between MC4R polymorphic site and breeding value for average daily gain (ADG, p<0.05) was observed. PRKAG3 polymorphic sites were also found to be significantly related to breeding values for ADG, AA, AB genotype (p<0.05) and also, for Backfat thickness (BF), days to 70 kg and BB genotype (p<0.05). In conclusion, selection method would be more effective if it encompasses significant genotype for performance traits and that would further aid in the selection of seed stock in KNP.