The molecular identification and histopathology are described for the parasitic larvae of a nematode species present in the abdominal cavity of Atlantic salmon (Salmo salar) grilse caught in fish traps on their natal river in the west of Ireland and post-smolts collected during experimental trawls on the continental shelf edge of the northeast Atlantic Ocean. Larvae in the adult and juvenile salmon were identified as Anisakis simplex sensu stricto by PCR amplification and RFLP and sequencing of the ITS gene and PCR amplification and sequencing of the cox2 gene. Parasitic nematode larvae in the grilse were either encapsulated in the abdominal mesentery associated with the pyloric ceca or on the serosal surface of the liver and in the vent region. In some fish, larvae were found in the parenchyma of the liver and muscularis circularis of the intestine. In general, the larvae induced a limited cellular response apart from the occurrence of focal melanin macrophage aggregates and individual eosinophilic granular cells in the connective tissue capsule. Melanin macrophage aggregates were also present among the hepatocytes adjacent to encapsulated larvae in the liver. The reaction to the parasites was more severe in the wall of the intestine. Encapsulated nematode larvae caused displacement, vacuolation, and necrosis of the circular muscle fibers. The stratum compactum was also disrupted with focal areas of degeneration. Overall, the intestinal wall had a hypercellular appearance with extensive cellular infiltration comprising eosinophilic granular cells, macrophages, lymphocytes, and fibrocytes. The post-smolts were caught in May during the early oceanic phase of their life cycle. In these fish, A. simplex sensu stricto larvae were found lying free on the serosal surface of the intestine and liver without any apparent histologic changes. This is the earliest in the marine migration of Atlantic salmon that A. simplex sensu stricto infection has been recorded.