CART (cocaine- and amphetamine-regulated transcript) peptides are neuromodulators that are involved in appetite control and energy homeostasis. It can inhibit food intake and reduce body weight that have received much attention, but a direct and comprehensive relationship with pigs differing in fatness which could be applied to breeding well has not been established. This study aims to search for polymorphism within the porcine CART gene and evaluate the effect of specific genotypes with regards to an association with fatness traits in a F2 population consisting of 230 individuals. Screening of 2264 bp DNA fragment covering the entire CART gene revealed 29 mutations and four indels (insertion or a deletion), in which four unlinked SNPs (single-nucleotide polymorphisms) could be digested by enzymes and subsequently genotyped in two purebreds and a F2 population. Landrace (lean-type), one of purebreds, presented significantly higher CART expression level than Lantang (obese-type) in most tissues studied. Association analysis revealed that three SNPs (T415C, C640T and C847T) displayed significantly association (p < 0.05) with fatness traits. Additionally, they are in almost complete linkage disequilibrium. Western blotting experiments on these three SNPs loci revealed difference in CART expression among individuals with different genotypes, and the individuals with lower average live backfat thickness (BFAW) expressed CART protein at a bit higher level than others. Our study screened and mapped the genetic variations in the porcine CART gene, and confirmed three functional SNPs which are promising molecular markers for pig production traits.