In this study, the ontogenetic trajectories of septal spacing between succeeding chambers of five modern cuttlefishes, Sepia esculenta, S. lycidas, S. latimanus, S. pharaonic and Sepiella japonica, which were all wild‐caught around Japan, were analysed. The ontogenetic trajectories of septal spacing of all examined cuttlefishes demonstrate a decrease in septal spacing followed by an increase during the earliest ontogenetic stage. This trend is assumed to be related to hatching. After the rapid decrease and increase in septal spacing, species‐dependent trends occur irrespective of sex and locality. Based on cluster analyses of general trends recognized in each species, the five examined species can be categorized into two groups: (1) a group by S. pharaonis, S. esculenta and Sepiella japonica; and (2) S. latimanus and S. lycidas as more distant branching groups within the five examined species. This classification is concordant with some phylogenetic clades determined from DNA analyses. Therefore, we hypothesized that the ontogenetic trajectories of septal spacing among modern cuttlefishes are phylogenetically dependent. If this hypothesis holds in fossil cuttlefishes, the examination of ontogenetic trajectories of septal spacing would give new insight into the recognition not only of the life history but also of the phylogeny of fossil cuttlefishes.