Motile Aeromonas septicemia (MAS) is a burden for striped catfish (Pangasius hypophthalmus) farmers in Vietnam. A. hydrophila is considered the leading cause of MAS in aquaculture but MAS can be caused by several species of Aeromonas. We obtained 86 isolates from diseased striped catfish fingerlings from nine provinces in Vietnam. The species identification was done using PCR, MALDI-TOF and analyzing the sequenced genomes. The MIC of commonly used antimicrobials was established using broth microdilution. After PCR, many isolates lacked the expected band size and all isolates were analyzed in MALDI-TOF. Thirty presumed A. hydrophila isolates were selected for whole genome sequencing and further characterization. Species identification based on sequencing established that 25/30 isolates were A. dhakensis ST 656 and 5/30 isolates were A. hydrophila ST 251. In the phylogenetic analysis, all publicly available A. dhakensis and A. hydrophila genomes from striped catfish in Vietnam had the same mentioned sequence types. The A. hydrophila ST 251 genomes differed with less than 200 SNPs and the A. dhakensis differed less than 100 SNPs. The tetracycline resistance gene tet(A) was found in 20 genomes and 19/20 of these isolates had an MIC = 8 mg/L. The phenicol resistance gene floR was found in 14 genomes and these isolates had an MIC > 8 mg/L. The virulence genes aerA/act, ahh1 and hlyA were present in all genomes. The ast gene was only present in A. dhakensis. The A. hydrophila genomes carried virulence genes coding for Flp type IV pili. None of the A. dhakensis carried genes coding for this type. The dominating Aeromonas spp. causing MAS in striped catfish fingerlings in Vietnam in the period studied was A. dhakensis. Likely, the importance of A. hydrophila as an aquaculture pathogen has been systematically overestimated as most routinely used identification methods are not able to differentiate between these two species. The current vaccine approved for use against MAS in Vietnam is based on A. hydrophila strains. It remains to be determined if there is a difference in the efficacy and effectiveness of this vaccine between fish infected with A. hydrophila compared to A. dhakensis.