Cultured stocks of Arctic charr Salvelinus alpinus and European grayling Thymallus thymallus are vulnerable to infection by achromogenic atypical Aeromonas salmonicida (AAS). In Finland, natural stocks of both fish species have to be supported by restocking, and AAS infection poses a threat to successful restocking because no preventive means are available. In this study, we analysed AAS isolates from Arctic charr and European grayling and from other sources genetically, and characterised the signs and pathology of AAS infection in Arctic charr and European grayling both under farming conditions and after experimental challenge. AAS outbreaks were recorded in 1 fish farm over an 8 yr period. Among various salmonid fishes under farming conditions, only Arctic charr and European grayling were susceptible to AAS infection. The disease caused by AAS could be reproduced in both species using the same AAS strain in an experimental challenge. The course of the disease and pathology of natural and experimental AAS infection differed between the 2 species, even though only 1 strain was used for challenge. Isolates of AAS from Arctic charr and European grayling were genetically identical within a single river water basin. However, genetic heterogeneity was observed among the isolates from different water basins. In both species, AAS caused systemic infection. The results suggest that the same AAS strain could be used to develop a vaccine to protect both Arctic charr and European grayling from AAS infection.