Some parasite species alter the behavior of intermediate hosts to promote transmission to the next host in the parasite's life cycle. This is the case for Euhaplorchis californiensis, a brain-encysting trematode parasite that causes behavioral changes in the California killifish (Fundulus parvipinnis). These manipulations increase predation by the parasite's final host, piscivorous marsh birds. The mechanisms by which E. californiensis achieves this manipulation remain poorly understood. As E. californiensis cysts reside on the surface of the killifish's brain, discerning regional differences in parasite distribution could indicate mechanisms for host control. In this study, we developed a method for repeated experimental infections. In addition, we measured brain-region specific density using a novel methodology to locate and quantify parasite infection. We show that E. californiensis cysts are non-randomly distributed on the fish brain, aggregating on the diencephalon/ mesencephalon region (a brain area involved in controlling reproduction and stress coping) and the rhombencephalon (an area involved in controlling locomotion and basal physiology). Determining causal mechanisms behind this pattern of localization will guide future research examining the neurological mechanisms of parasite-induced host manipulation. These findings suggest that parasites are likely targeting the reproductive, monoaminergic, and locomotor systems to achieve host behavioral manipulation.