The ecological effects of predator removal and its consequence on prey behavior have been investigated widely; however, predator removal can also cause contemporary evolution of prey resulting in prey genetic change. Here we tested the role of predator removal on the contemporary evolution of prey traits such as movement, reproduction and foraging. We use EcoSim simulation which allows complex intra- and inter-specific interactions, based on individual evolving behavioral models, as well as complex predator–prey dynamics and coevolution in spatially homogenous and heterogeneous worlds. We model organisms' behavior using fuzzy cognitive maps (FCM) that are coded in their genomes which has a clear semantics making reasoning about causality of any evolved behavior possible. We show that the contemporary evolution of prey behavior owing to predator removal is also accompanied by prey genetic change. We employed machine learning methods, now recognized as holding great promise for the advancement of our understanding and prediction of ecological phenomena. A classification algorithm was used to demonstrate the difference between genomes belonging to prey coevolving with predators and prey evolving in the absence of predation pressure. We argue that predator introductions to naive prey might be destabilizing if prey have evolved and adapted to the absence of predators. Our results suggest that both predator introductions and predator removal from an ecosystem have widespread effects on the survival and evolution of prey by altering their genomes and behavior, even after relatively short time intervals. Our study highlights the need to consider both ecological and evolutionary time scales, as well as the complex interplay of behaviors between trophic levels, in determining the outcomes of predator–prey interactions.