Through a functional genomic analysis for glycosidase, we identified a candidate alpha galactosidase in the genome of Elizabethkingia meningoseptica. The gene was cloned and expressed in Escherichia coli (E.coli). The purified protein was subjected to assays with synthetic p-nitrophenol (pNP) substrates for its enzymatic properties. The results indicated that it had alpha-linked galactose (α-Gal) substrate specificity. The optimum pH was between 3.0 and 8.0, and the optimum temperature was between 4 and 45 ℃. Further assays with oligosaccharide substrates and Mass Spectrometry analysis found that this enzyme could digest the terminal α-1，3/1，4/1，6Gal, respectively. In addition, we also demonstrated that the enzyme can efficiently remove the terminal Galα1-3Gal antigen presented on porcine erythrocytes to alleviate hyperacute immune rejection in heterologous blood transfusion. As terminal alpha galactose modification plays an important biological role in immunity and infection, the reported alpha galactosidase may serve as a new tool for research in this field.