Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and brought huge economic damages to the local salmonid aquaculture in China. An ASM strain named AS‐C4 was used to investigate the colonization of ASM in Atlantic salmon (Salmo salar L.) by an immersion challenge with the control group (T0, no AS‐C4), group T1 (2.67 × 104 CFU/ml AS‐C4) and group T2 (2.67 × 107 CFU/ml AS‐C4). The numbers of AS‐C4 copies in different fish tissues (gill, intestine, skin, blood, muscle, spleen, liver and kidney) were determined at different time points post challenge using the quantitative real‐time PCR (qRT‐PCR). AS‐C4 were detected in the gill and intestine as early as 0 hr after the challenge both in T1 and T2 groups, suggesting that the gill and intestine were probably the portals of entry of AS‐C4 into salmon. Although AS‐C4 could not be detected in the skin until 24 hr after the challenge in T1 group, it could be detected in the skin as early as 0 hr after the challenge in T2 group, indicating that the skin may also be a portal of entry of AS‐C4 into salmon. AS‐C4 was immediately detected in the blood within 3 hr after it entered the host, suggesting that AS‐C4 successfully invaded the bloodstream of fish. After AS‐C4 colonized the host, it colonized the internal tissues, such as the spleen, liver, kidney and muscle. The results of this study will contribute to the understanding of the pathogenesis of the ASM strains and give a broader understanding of the infection route of ASM in it's host, providing more information for the development of new therapeutic strategies to protect against this pathogen in aquaculture.