To date, blaNDM and blaKPC genes have been found predominantly in clinical settings around the world. In contrast, bacteria harbouring these two genes from natural environments are relatively less well studied compared to those found in clinical settings. In this study, a carbapenem-resistant Raoultella ornithinolytica strain, WLK218, was isolated from urban river sediment in Zhengzhou City, Henan Province, China. This isolate was subjected to PCR and antimicrobial susceptibility testing. PCR results showed that this isolate was positive for both the blaNDM-1 and blaKPC-2 genes. The antimicrobial susceptibility testing results showed that this isolate exhibited resistance or intermediate resistance to all the antibiotics tested except for streptomycin (susceptible) and cefepime (susceptible-dose dependent). The complete genome sequence of the WLK218 isolate was then determined by using a combination of the PacBio and Illumina sequencing technologies. The de novo assembly of the genome generated one chromosome and six plasmids. Among the six plasmids, the blaNDM-1 gene was carried on the IncX3 plasmid pWLK-NDM, while the blaKPC-2 gene was located on the untypeable plasmid pWLK-KPC. This is the first report of an environmental Raoultella ornithinolytica isolate co-harbouring the blaNDM-1 and blaKPC-2 genes.