This study was carried out to identify SNP associated with fatness traits on pig chromosome 6. In total, 11,067 putative genomic variations were detected in 125 complete bacterial artificial chromosome sequences corresponding to the region between SW2098 and SW1881, which harbors multiple QTL affecting intramuscular fat content (IMF) and backfat thickness (BFT). Among 173 putative SNP validated by MassArray, 120 SNP were used in an association study on 541 offspring produced by a cross of Korean native pig and Landrace breeds. The significance level of each SNP was determined using single marker regression analysis. Further, significant threshold values were determined using a false discovery rate. Nine out of 120 SNP showed significant effects on BFT or IMF or both. Of the 9 significant SNP, 4 were significantly associated with IMF, 7 were significantly related to BFT, and 2 SNP (Kps8172 and Kps6413) showed significant effects on both traits. Moreover, multiple regression analysis considering all significant SNP was used to correct spurious false positives due to linkage disequilibrium. Consequently, only 1 SNP (Kps6413) was significant for IMF, whereas 4 SNP including Kps6413 showed significant effects on BFT. The significant SNP had generally additive effects and on average explained 1.72% of the genetic variation for IMF and 3.92% for BFT, respectively. These markers can potentially be applied in pig breeding programs for improving IMF and BFT traits after validation in other populations.