The use of phase coherence between two pings is used in many underwater imaging applications, in particular the micronavigation algorithms used in correcting receiver positions when focussing a synthetic aperture sonar (SAS) array. Recently, interest has turned to using the phase coherence between two sonar images that consist of two repeated passes over the same area in order to co-register the images and perform coherent change detection, meaning the detection of differences in two areas that causes a decorrelation between the two images. Such techniques are used in synthetic aperture radar (SAR) applications, and can detect subtle changes that are not immediately detectable by visual inspection or other traditional methods. Before computing the coherence the two images have to be accurately co-registered. Indeed remaining misregistrations after a 2D rigid translation lead to a loss of phase coherence. This can be due to navigational disturbances or data processing defects. The problem of non-rigid and subpixel sonar image registration is achieved here in two main steps. The first step aims to estimate the displacement field from which a warping function is derived; then, the repeat-pass image is resampled using the warping function to co-register it to primary image