The objective of this work was to isolate the polygalacturonase genes of Galactomyces citri-aurantii IJ-1 harvested from rotten citrus peels and to heterologously express these genes in Pichia pastoris. Two polygalacturonase (PG) genes from G. citri-aurantii IJ-1 were obtained and tentatively named PG1 and PG2. The genes were cloned into $pPICZ{alpha}C$, and expressed in Pichia pastoris strain GS115 with a native signal peptide or the ${alpha}$-factor secretion signal peptide of Saccharomyces cerevisiae. All of the recombinant proteins were successfully secreted into the culture media and confirmed as a single band with a molecular weight of 35 to 38 kDa by SDS-PAGE. The specific enzyme activities of recombinant PG1 and PG2 purified by His-tag affinity resin were 4,749 and 6,719 U/mg, respectively, with an optimal pH and temperature of pH 4.0 and $50^{circ}C$. The Michaelis-Menten kinetic constants for PG1 and PG2, $K_m$, were confirmed to be 0.94 and 0.84 mM, respectively. In the presence of $Mn^{2+}$, the activity of PG1 and PG2 were increased to 160.8 and 146.4% of normal levels, respectively. In contrast, $Cu^{2+}$ and $Fe^{3+}$ acted as strong inhibitors to the PGs.