Daphnia's antipredator responses are regulated largely by the nervous system, making these responses particularly susceptible to compounds that impact neurodevelopmental or neurofunctional processes. This study aimed to determine the molecular pathways involved in modulating the effects of scopolamine on inducible antipredation responses triggered by fish kairomones. We used two clones showing two contrasting responses. The positive phototactic clone 85 responds strongly to fish kairomones showing a marked negative phototactism and higher developmental rates. Consistently, the negative phototactic clone F shows the opposite behavior to the same stimuli. Adults of both clones were exposed to fish kairomones, scopolamine alone and a mixture of both. Scopolamine is a muscarine antagonist able to mimic fish kairomones inducible behavioral responses in both clones, while affecting differently morphological and life-history traits. Whole transcriptomic Illumina analyses indicated a greater number of de-regulated genes of the fish kairomone sensitive clone 85 (1650) compared to the F one (1138), which were grouped in four clusters (two per clone). The mixture of scopolamine and fish kairomone treatments on gene transcription was additive in both clones, indicating similar modes of action. Most enriched metabolic routes were related with neurological pathways and regulation of cell proliferation/differentiation. Our results indicate that fish kairomones and scopolamine deregulate not only neurological signaling pathways but also cell differentiation and proliferation pathways, which are linked to the observed behavioral responses as well as the developmental, morphological, and reproductive effects.