In an inkjet printer, a first printhead forms a first mark on a print medium using a high-contrast ink. A second printhead forms a second mark on the first mark using a low-contrast ink. The printer generates image data of the low-contrast ink mark and the high-contrast ink, and a controller in the printer identifies a cross-process direction offset between the first printhead and the second printhead with reference to a distance between the center of the first mark and the second mark in the image data.