The differential EST of small intestine tissue was investigated in Chinese native pig breeds and DLY(Duroc×Large white×Yorkshire) using DDRT-PCR. Total mRNA in small intestine tissue were extracted and reversely transcribed into cDNA. 18 primer pairs combinated by three anchor primers and six random primers were employed for differential display of reverse transcriptional polymerase chain reaction (DDRT-PCR). The PCR products were sequenced and then the differential EST and its SNPs were analyzed. The results showed that more than 180 EST sequences were obtained, including 6 inter-individual differential ESTs of the local pig breed, 12 inter-individual differential ESTs of the DLY pigs. Eight differential ESTs between the local breed and DLY pig were detected in which 3 typical differential ESTs, G24-300, G01-360 and A12-340, were selected for further research. The expression level of G24-300 in the DLY was higher than that in local pigs, while the expression levels of G01-360 and A12-340 EST didn't differ between two pig-types. G01-360 had rich SNPs, and showed the difference between native pig breed and DLY.