Abstract: 【Objective】Clarify the BMP2 and FGFR3 genes sequences and expression differences between Guangxi Bama mini pig and Landrace pig, and provide theoretical basis for elucidating the formation mechanism of large and small pigs.【Method】The growth plate cartilage tissue of appendicular skeleton from one-day-old Guangxi Bama mini pig and Landrace pig was used to extract total RNA. After that, the total RNA was reverse transcribed to synthesize cDNA and then used for PCR amplification of the coding region(CDS) sequence of BMP2 and FGFR3 genes. PCR-RFLP was used to detect the polymorphism of the SNP locus of FGFR3 gene. The expression differences of FGFR3 and BMP2 in one-day-old Guangxi Bama mini pig and Landrace pig were compared by real-time fluorescence quantitative PCR.【Result】The results indicated that the body type of one-day-old Guangxi Bama mini pig and one-day-old Landrace pig were greatly different, and the differences in body weight, body length and body height were extremely significant(P<0.01, the same below), and the difference in femoral length reached a significant level(P<0.05, the same below). A full length of BMP2 gene CDS with 1188 bp was cloned from Guangxi Bama mini pig and Landrace pig, respectively, and the CDS sequence between the two breeds were completely consistent. The CDS sequence of FGFR3 gene with 808 bp cloned from Guangxi Bama mini pig and Landrace pig were found to have 8 base mutations and 1 base deletion when compared with the published FGFR3 sequence from NCBI(XM_005666479.1). Five mutations, which were A124 G, C190 G, A204 C, C205 A and C245 T missense mutations, were detected in Bama mini pig and Landrace pig, and A438 G and C549 T synonymous mutations in Guangxi Bama mini-pig and A752 C missense mutation in Landrace pig were found, respectively. There were 328-330 base(GCA) deletion in Landrace pig. The genotype and gene frequency of FGFR3 gene in A2374 G and C2620 T loci were extremely significant difference between Guangxi Bama mini pig and Landrace pig. The corresponding allele distributions were not in accordance with Hardy-Weinberg equilibrium, but the two loci were in the state of linkage disequilibrium. Compared to Landrace pig, the cartilage tissue of the growth plate of one-day-old Bama mini pig had significantly lower BMP2 expression, but the FGFR3 gene expression level was extremely significantly higher than that of Landrace pig.【Conclusion】BMP2 gene and FGFR3 gene have important significance in the formation of cartilage and bone. Among them, BMP2 promotes the development of pig bone, and FGFR3 gene inhibits the development of pig bone. It is speculated that the short size of Guangxi Bama mini-pig is directly related to the high expression of FGFR3 and the low expression of BMP2.