A morphological dataset based on 14 standard counts and indices was constructed for 68 specimens comprising 12 species of octopuses. This was used to construct distance matrices based on morphological characters. These matrices were compared with genetic distance matrices compiled during molecular phylogenetic analyses of the same 12 species using four mitochondrial and two nuclear genes. Mantel tests showed that there was significant congruence between the phenetic and genetic matrices, suggesting that the genetic signal is reflected in the morphological data set. Matrices of geographical distance were constructed for the 12 species based on the latitude, longitude, and depth of capture of 1726 individuals. These matrices never showed significant congruence with genetic data or with morphological data. Multivariate analysis of the morphological dataset suggests that these counts and indices, traditionally used for discriminating between species in cephalopods, do not show great discrimination at species level, but provide excellent discrimination at the generic level, and, as such, might be useful for resolving the generic placement of some problematic taxa.