One of the most entrenched binary oppositions in archaeology and anthropology has been the agriculturalist vs hunter-gatherer-fisher dichotomy fuelling a debate that this paper tackles from the bottom-up by seeking to reconstruct full past diets. The Japanese prehistoric Jōmon cultures survived without fully-developed agriculture for more than 10,000 years. Here we compile a comprehensive, holistic database of archaeobotanical and archaeozoological records from the two ends of the archipelago, the northernmost prefecture of Hokkaido and the southernmost island-chain of Ryukyu. The results suggest Jōmon diets varied far more geographically than they did over time, and likely cultivated taxa were important in both regions. This provides the basis for examining how fisher-hunter-gatherer diets can fulfil nutritional requirements from varied environments and were resilient in the face of environmental change.