A genetic survey was carried out on recently emerging fry to investigate interbreeding between anadromous and freshwater resident brown trout in La Roche Brook, a major spawning tributary of the Oir River system (Normandy, France). Emerging fry were sampled at three different sites in spring 2002 and 2003. Stable isotope analysis (SIA) allowed the classification of each individual as the progeny of resident (N = 76) or anadromous (N = 58) female trout. Microsatellite DNA analysis showed that genetic diversity between fry samples can be explained by microgeographical (various sampling sites) and temporal (2 years of sampling) variations rather than maternal origin (anadromous vs. freshwater resident). We conclude that a high level of gene flow exists between the two morphs when anadromous adults have access to the spawning grounds of residents. We highlight the relevance of using SIA in conjunction with genetic analysis to study interactions between the two morphs.