We previously reported the purification of an acid phosphatase (APase52) secreted from the mycelia of Pholiota nameko under phosphate-deficient conditions. In the present study, two other isozymes (APase47 and APase48) were found and their structures were compared with that of APase52. Thirteen amino acid residues at the N-terminus of APase47 were completely identical with those of APase48 and had partial homology with those of APase52. The deglycosylation of proteins indicated that three APase isozymes differ in the N-linked oligosaccharide content. The protease-generated peptide maps of the APases differed from one another in the band pattern. These results suggest that the APases are the products of different genes.