We observed 1E 1207.4--5209, a neutron star in the center of the supernova remnant PKS 1209--51/52, with the ACIS detector aboard the Chandra X-ray observatory and detected two absorption features in the source spectrum. The features are centered near 0.7 keV and 1.4 keV, their equivalent widths are about 0.1 keV. We discuss various possible interpretations of the absorption features and exclude some of them. A likely interpretation is that the features are associated with atomic transitions of once-ionized helium in the neutron star atmosphere with a strong magnetic field. The first clear detection of absorption features in the spectrum of an isolated neutron star provides an opportunity to measure the mass-to-radius ratio and constrain the equation of state of the superdense matter.