Aeromonas species are responsible for the disease motile Aeromonas septicemia (MAS) in striped catfish (Pangasius hypopthalmus). A. hydrophila is so far considered the most common cause of MAS in Vietnam, but other species have also been isolated from diseased fish. We analyzed 86 bacterial isolates collected from the kidneys of striped catfish with MAS symptoms. The isolates were collected over a 5-year period (2017-2021) from nine provinces in the Mekong Delta. Sixty-eight isolates were identified as A. hydrophila by MALDI-TOF while remaining isolates belonged to other Aeromonas spp.. The minimum inhibitory concentration (MIC) of all isolates was determined for 14 antimicrobials. Thirty representative isolates were selected for whole genome sequencing (WGS) based on their sampling year and province of origin. Surprisingly, from the WGS analysis, only 5/30 isolates were confirmed as A. hydrophila while 25/30 isolates were identified as A. dhakensis, making A. dhakensis the predominant species in the analyzed collection. All of the A. hydrophila isolates belonged to sequence type (ST) 251 and all A. dhakensis belonged to ST 656. This finding was also supported by the phylogenetic analysis where isolates of one species grouped in a separate cluster (Fig. 1). All of the A. hydrophila isolates had an MIC ≤ 0.12 for enrofloxacin, ≤ 2 for tetracycline and oxytetracycline and ≤ 1 for florfenicol. For A. dhakensis the MIC ranged from ≤ 0.12 – 2 for enrofloxacin, ≤ 0.12 – > 8 for tetracycline and oxytetracycline, and ≤ 1 – > 8 for florfenicol. The strains harbored resistance genes like sul1, sul2 and floR (Fig. 1). All genomes carried genes coding for translocation of proteins (type two and type six secretions systems), motility (polar flagella), motility and adherence (Tap type IV pili) and genes coding for aerolysin and cytolytic enterotoxin (aer and act). Additionally, all A. hydrophila isolates carried genes coding for biofilm and autoagglutination (Flp type IV pili) and cytotonic enterotoxin (ast). Each of the mentioned virulence factors contributes to the virulence of Aeromonas spp.. A nucleotide BLAST of the contigs where resistance genes were located revealed that the sul2, qnrS2 and floR genes were plasmid mediated. Because A. hydrophila has been considered the leading cause of MAS, current vaccines include A. hydrophila strains. Our study indicate that A. dhakensis is the dominating species associated with MAS in the Mekong Delta, but further studies of this apparent change in species are warranted, e.g. A. dhakensis needs further characterization and it should be determined if current vaccines also protect against A. dhakensis. Improved methods for correct identification of the different Aeromonas species are needed.