The dwarf cuttlefish, Sepia bandensis, a small cephalopod that exhibits dynamic camouflage, is an emerging model organism in neuroscience. Coleoid cephalopods (cuttlefish, octopus, and squid) evolved large, complex brains capable of learning, problem-solving, and memory. We used high resolution magnetic resonance imaging (MRI), deep learning, and fluorescent histology to generate a dwarf cuttlefish brain atlas and built an interactive web tool (cuttlebase.org) to host the data. Guided by observations in other cephalopods, we identified 38 brain lobes. The dwarf cuttlefish brain is partially encased in cartilage and includes two large optic lobes (74% the total volume of the brain), chromatophore lobes whose motor neurons directly innervate the skin, and a vertical lobe that has been implicated in learning and memory. Motor neurons emerging from the chromatophore lobe modulate the color, pattern, and texture of the skin to elicit camouflage. This brain atlas provides a valuable tool for exploring the neural basis of cuttlefish behavior.