Sea-reared rainbow trout production in Denmark currently struggles with furunculosis, a septicemic infection caused by the bacterium Aeromonas salmonicida subs. salmonicida. Developing an effective control strategy is vital for future production, though it requires having knowledge of the epidemiology, as well as the genetic and virulent variability of the homogenous Danish A. salmonicida isolates. In order to obtain this knowledge, 101 A. salmonicida, including 99 Danish isolates, one Scottish strain and the type strain NCIMB 1102, were sequenced using the Illumina MiSeq platform. Isolates were de novo assembled, examined for presence of plasmids, virulence and iron acquisition proteins, antibiotic resistance genes and SNPs that were aligned and subjected to Bayesian temporal phylogenetic and maximum likelihood tree reconstruction using the published genome of A. salmonicida A449 as reference. Bayesian temporal phylogenetic reconstruction showed that four major introductions of A. salmonicida into Denmark have occurred. The introductions correlate with the freshwater and subsequent seawater expansion of rainbow trout production. Initial transmission of the bacterium could have been from seawater to freshwater or vice versa, both scenarios are open and most minor clades include a mixture of different fresh- and seawater farms. Genetic variation of A. salmonicida is mostly associated with their plasmidome and plasmid encoded virulence factors. Nine A. salmonicida harbored worldwide known ARGs against several antibiotics. These findings provide novel information regarding the Danish A. salmonicida population and demonstrate that WGS is a highly useful tool for studying homogenous bacteria such as A. salmonicida.