Activation in the hippocampus (HC) and prefrontal cortex (PFC) is critical to accurately retrieve overlapping sequences. Experiments 1 and 2 tested the hypotheses that activation in and interaction between HC and PFC increases as overlap between sequences increases in a non-spatial task. Experiment 3 tested the hypothesis that theta oscillations are involved in orchestrating interactions between HC and PFC in a spatial task with overlapping elements. In the first two studies, 17 participants (aged 18-34; 11 female) learned sequences consisting of a picture frame, face, and scene. Conditions varied by degree of overlap. Using fMRI, Experiment 1 tested how degree of overlap affected HC and PFC activation. In overlapping sequences, middle and posterior HC were active when predictability of the correct response increased, dorsolateral PFC was active when participants were able to ascertain the correct set of sequences, and ventrolateral PFC was active when inhibition of interfering associations was required. Experiment 2 examined functional connectivity of HC and PFC during disambiguation. Low- and high-overlap conditions were associated with increased connectivity in separate regions at different times indicating that retrieval under the two conditions used different neural networks and strategies. Low-overlap trials were associated with increased connectivity between HC and prefrontal and parietal regions. High-overlap trials showed increased connectivity between lateral PFC and visual areas, indicating that imagery may be necessary for accurate performance. Using EEG recording, Experiment 3 examined theta activity during retrieval of well-learned, overlapping and non-overlapping mazes in 17 participants (aged 18-34, 11 female). Theta activity increased in overlapping mazes during the first of four hallways, suggesting participants were looking ahead to upcoming turns in the maze. Theta activity increased at the beginning and choice point of the third overlapping hallway, possibly in response to interference from the paired, overlapping maze. These studies provide evidence that (1) overlapping associations in non-spatial sequences elicit interactions between hippocampus and lateral prefrontal cortex, (2) increasing the degree of overlap changes the neural processes required to perform the task, and (3) theta power increases in response to increased cognitive demand and maintenance of sequence information needed to differentiate between overlapping spatial routes.