New Zealand rattail fish are of great interest both to biologists who study their phylogenetics and in fisheries. In contrast, their morphological evolution is little studied and poorly understood. Geometric morphometric methods based on scale shape were applied in this study to determine differences among species and genera. Scale shapes were described using seven landmarks, the coordinates of which were subjected to a generalized Procrustes analysis, followed by a principal components analysis. A cross-validated discriminant analysis was applied to assess and compare the size-shape (centroid size plus shape variables) efficacy in the species and the discrimination of the genera. Two main phenetic groups were identified: cluster no. 1 with eight species and cluster no. 2 with six species. Coelorhinchus aspercephalus and Mesovagus antipodum were more separated from the other species in the first cluster. The cross-validated canonical discriminant analysis correctly classified 74% at the genus level, with most misclassifications occurring between Coelorhinchus and Coryphaenoides, whereas the best classified genera were Mesovagus and Trachyrincus. The discrimination of correctly classified species ranged from 41.2 to 100%. The highest correct classification rates were recorded for Coryphaenoides armatus, Coelorhinchus innotabilis, Trachyrincus longirostris and Mesovagus antipodum.