Abstract Cuttlefishes, like their octopus cousins, are masters of camouflage by control of body pattern and skin texture to blend in with their surroundings for prey ambush and threat avoidance. Aside from significant progress on the cuttlefish visual perception and communication, a growing number of studies have focused on their behavioural neurobiology and the remarkably rapid and apparently cognitively complex reactions to novel challenges such as spatial learning to solve maze tasks and vertebrate-like cognitive capabilities (e.g. object recognition, number sense and episodic-like memory). Despite intense interest of cuttlefish, much of our knowledge of its neuroanatomy and links to behaviour and ecology comes from one temperate species, the European common cuttlefish, Sepia officinalis. Here we present the first detailed comparison of neuroanatomical features between the tropical cuttlefish and squid and describe differences in basic brain and wiring anatomy using MRI-based techniques and conventional histology. Furthermore, comparisons amongst nocturnal and diurnal cuttlefish species suggest that the characteristic neuroanatomical features infer interspecific variation in visual capabilities, the importance of vision relative to the less utilised chemosensory system and clear links with life modes (e.g. diurnal vs nocturnal), ecological factors (e.g. living depth and ambient light condition) as well as to an extent, phylogeny. These findings link brain heterogeneity to ecological niches and lifestyle, feeding hypotheses around evolutionary history and provide a timely, new technology update to older literature.