A method and system for estimating color separation misregistration of a printing system. The method may include marking a substrate to form a misregistration estimation patch. The misregistration estimation patch being formed by first and second color separations. The first color separation marking the substrate with a first halftone pattern. The first halftone pattern has a first halftone-frequency vector in a first direction and a second halftone-frequency vector in a second direction. The second color separation marking the substrate with a second halftone pattern. The second halftone pattern has a first halftone-frequency vector in a first direction and a second halftone-frequency vector in a second direction. The first and second halftone patterns form a moiré pattern. A deviation in at least one the halftone frequency vectors and/or the moiré pattern can be indicative of a color separation misregistration. The method also includes estimating the color separation misregistration of the printing system using the misregistration estimation patch.