Cephalopods are variable and very interesting animals, including octopuses, squids, cuttlefish, and nautiluses. They are deemed to be the most intelligent invertebrate group known to taxonomy. Cephalopods are underrepresented in both genome sequencing projects as well as baraminology studies. However, mitochondrial genome sequences for 47 cephalopod species as well as morphological character data sets are available for this group of invertebrate animals, two of which were used in this study. Using sequence alignment and clustering methods on whole mitochondrial genome sequences, five putative baramins were discovered—octopuses, squids I and II, cuttlefish, and nautiluses. However, even though analyzing the mitochondrial genome may have its advantages, the mitochondrial genome is only less than 0.01% of the nuclear genome, and does not contain enough information to draw final conclusions. The results from the genome analysis study were augmented with the analysis of two morphological character sets which, when combined cover 72 cephalopod species, even fossil taxa which represent the palaeobaramin. In total, 106 species were studied by at least one method. The first morphological analysis suggests that Decapods and Octopods each form a single holobaramin, whereas the second morphological analysis suggests that nautiluses form a separate, third holobaramin within the class Cephalopoda. These results are interesting; however, it would still be useful to further analyze cephalopod baramins in order to get a fully clear picture of the baraminic relationships within this class of invertebrate species.