Abstract: In order to identify the pathogen and its characteristics in diseased Cuora flavomarginata in Hangzhou, Zhejiang, in June 2020, a dominant strain HZ202006 was isolated from the liver of the diseased turtles. Morphological observations, 16S rRNA sequence analysis, whole-genome sequencing, artificial infection experiments, and antimicrobial sensitivity test were performed on this strain. The results confirmed that the strain is Providencia rettgeri, a short rod-shaped, Gram-negative bacterium. Whole-genome sequencing revealed that the complete genome sequence of this strain consists of a 4.8 Mbp double-stranded DNA and two plasmids. Annotation of the sequenced genes using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factors Database (VFDB) identified 20 resistance genes and four virulence factors in the bacterium. Antimicrobial sensitivity test demonstrated that HZ202006 was moderately sensitive only to amikacin, and resistant to 16 common antibiotics, including penicillin, cephalosporins, and aminoglycosides. This study isolated and identified a strain of P. rettgeri causing disease in C. flavomarginata, providing insights for disease control in aquaculture animals affected by this bacterium.