Estimating Minimum Number of Individuals (MNI) is a crucial prerequisite step of zooarcheological analyses, notably to determine taphonomic history of bone assemblages and function of sites. Isolated petrous bones of suids are frequently preserved in sites but identification of antimeric pairs is hindered by the difficulty to disentangle various components of morphological variability (right-left asymmetry, sexual dimorphism). We developed a new morphometric protocol to quantify morphological variation of lateral and medial faces of the petrous bone and identify antimeric pairs within samples of isolated petrous bones of suids. The new protocol combines 3D traditional and 2D geometric morphometrics on surface models from CT scans and standardized views from 3D models. We first tested this protocol on a sample of 30 petrous bones of extant suids (Sus scrofa, Phacochoerus africanus), including six antimeric pairs from known individuals. By computing Mahalanobis distances between all possible pairs of petrous bones within that sample, we were able to identify a threshold of distances below which specimens belong to known antimeric pairs. We then applied the same protocol to a sample of 23 isolated petrous bones of the suid genus Metridiochoerus from the site of Ahl al Oughlam, Morocco. This Plio-Pleistocene site represents a useful non-anthropogenic bone assemblage to be compared to anthropogenic sites. We identified four likely antimeric pairs within the Ahl al Oughlam sample, allowing us to estimate a MNI of 19.