Relationships between apex predators and mesopredators have been poorly documented in predatory birds. Prediction from intraguild predation (IGP) theory suggests that following the recovery of Peregrine Falcon (Falco peregrinus) populations, the potential for Merlins (F. columbarius) to experience mesopredator suppression should increase where these species share habitat and prey resources. In Washington, both falcons prey on Dunlins (Calidris alpina) in estuarine ecosystems during the nonbreeding season. To investigate whether mesopredator suppression may have occurred, I compared aspects of the hunting behavior of Merlins at an estuary in western Washington between 1999 and 2009, when Peregrine Falcons were regularly present, with hunting behavior in the 1980s, when Peregrine Falcons did not occur at the site. Merlin hunting behavior changed substantially between the two periods. Following Peregrine Falcon recovery, Merlins hunted less frequently, used hunting flights of shorter duration and that involved fewer capture attempts per successful flight, and captured prey closer to the cover of vegetation, results that are consistent with IGP theory. Prior to Peregrine Falcon recovery, Merlins appear to have assumed the role of apex falcon predator at the site; Merlins currently coexist with Peregrine Falcons, and have altered their hunting behavior which may reduce their risk of IGP.