The three dimensional structure of Arabidopsis thaliana PAP-specific phosphatase was predicted by use of various existing methods on sequence comparison, secondary structure prediction, three dimensional structure prediction and simulation. It was a structure similar with that of Hal2p in Saccharomyces cerevisiae, consisting of an α＋β N-terminal domain and an α/β C-terminal domain. In the predicted structure, possible binding sites for Mg²⁺, as well as for other metal ions, and the structural base sensitive to Na⁺ were found. These sites were related with the biochemical function of Arabidopsis thaliana PAP-specific phosphatase. The structural and functional analysis suggested that the theoretical structure of Arabidopsis thaliana PAP-specific phosphatase, having been deposited in PDB, is not reasonable.