In this paper we provide a focused review of the literature examining neural mechanisms involved in cognitive control over memory processes that can influence, and in turn are influenced by, emotional processes. The review is divided into two parts, the first focusing on working memory and the second on long-term memory. With regard to working memory, we discuss the neural bases of (1) control mechanisms that can select against distracting emotional information, (2) mechanisms that can regulate emotional reactions or responses, (3) how mood state influences cognitive control, and (4) individual differences in control mechanisms. For long-term memory, we briefly review (1) the neural substrates of emotional memory, (2) the cognitive and neural mechanisms that are involved in controlling emotional memories and (3) how these systems are altered in post-traumatic stress disorder. Finally, we consider tentative generalizations that can be drawn from this relatively unexplored conjunction of research endeavors.