Ten polymorphic enzyme coding loci were assayed using starch gel electrophoresis in anadromous (sea trout) and freshwater‐resident trout,Salmo trutta, from two neighbouring river systems draining into Clew Bay in western Ireland. Samples were collected from the Burrishoole and from the neighbouring Newport river system. In the Burrishoole system, two samples were from above waterfalls impassable to migratory trout, two consisted of anadromous smolts or post‐smolts and the remainder were freshwater‐resident trout from freely accessible areas. There were large differences in gene frequency between trout from above impassable barriers and all others sampled, and these two groups also differed substantially from each other. More minor differences were evident between some other samples, particularly between trout from the upper lake and streams entering it and a stream associated with the lower lake. Two anadromous populations therefore occur in the Burrishoole system. In contrast, no differences were evident in two sampling years between anadromous trout and cohabiting freshwater‐resident trout from the upper part of the Burrishoole system. Thus, in the upper part of this system, anadromous trout do not appear to comprise a separate population from non‐migratory trout and interbreeding