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While it is established that behaviour can vary across genetically identical individuals, it remains unknown how much of this variation stems from momentary experience during learning compared to genetics and its past interactions with the environment. To address this, we measured behaviour in thousands of flies from 90 genetic backgrounds while they performed tasks in conditions that either did or did not require learning. Flies that were genetically identical, raised under the same conditions, and tested simultaneously in the same environment persistently modified the extent of expressed individuality when they could learn. This learning-induced residual expression of individuality and its dynamics were subdued or absent in innate, learning-independent behaviours. We could quantify and then recreate this phenomenon in computer simulations. The emergence of in silico behaviour individuality was most consistent with the individuality of real flies once we enabled reinforced learning in simulated agents. Moreover, we showed that minor differences in initial conditions of the experiment can exacerbate the expression of individuality within a genotype in a learning-dependent manner. 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