Objective To clone the coding sequence of Guangxi Bama mini-pig PGC-1α gene, and to analyze the expression of PGC-1α gene in various tissues of mini-pigs using RT-PCR and QRT-PCR techniques. Methods The PGC-1α gene coding sequence (CDS) was amplified by PCR from the cDNA of longissimus muscle of Guangxi Bama mini-pig. The PCR products were inserted into pEASY-T5 vector, transfected E. coli, identified and sequenced. The PGC-1α gene expression in different tissues of the Bama mini-pigs was detected by RT-PCR and QRT-PCR assays. Results The PGC-1α gene CDS of Guangxi Bama mini-pig was cloned. It was 2391 bp in length. It had 99.9% homology with the reference sequence, and had two synonymous mutations that were C-A1105 and G-A1524. The expression level of PGC-1α gene was higher in the heart and kidney, followed by liver, subcutaneous fat and longissimus muscle, but the expression was not detected in pancreas of Guangxi Bama mini-pig. Conclusions We have successfully cloned the PGC-1α gene of Guangxi Bama mini-pig, and detected this gene expression in six tissues. The results of this study will provide a basis for studying the effect of PGC-1α on type 2 diabetes mellitus (T2DM) in Bama mini-pigs.