There are few reports on bloodstream infections caused by Aeromonas dhakensis. This article presented a case report of a patient with liver cirrhosis who developed Aeromonas dhakensis bloodstream infection. The patient exhibited symptoms such as fever, cellulitis, necrotizing fasciitis, rhabdomyolysis, and lesions resembling pyoderma gangrenosum, and suffered septic shock. The disease progressed rapidly with a poor prognosis. During the species identification process, methods such as the bioMérieux VITEK 2 Compact identified the isolate as either Aeromonas hydrophila or Aeromonas caviae. The Bruker mass spectrometer identified it as Aeromonas hydrophila, noting that the intragenus protein fingerprint was similar and could not be differentiated from other species. Additionally, 16S rRNA sequencing failed to unequivocally distinguish the species. All these methods including the bioMérieux VITEK 2 Compact, Bruker mass spectrometer, and 16S rRNA sequencing were unable to provide accurate identification. However, gyrB sequencing and metagenomic next-generation sequencing (mNGS) were able to yield definitive species results. Through the comprehensive application of multiple methods, this study provides a clear identification result for clinical diagnosis.