The Klebsiella pneumoniae complex consists of seven species that are related to K. pneumoniae, including K. variicola, which may colonize a variety of hosts, including environmental sources. The importance of K. variicolainfection is obscured by imprecise detection methods, however, next generation sequencing technology has been used to correctly identify this species. Long-read sequencing is particularly helpful for the analysis of mobile genetic elements carrying antibiotic resistance genes, such as plasmids and bacteriophages. The K. variicola strain determined in this study was obtained from a wastewater treatment plant in the North West Province. Long reads sequencing using Oxford Nanopore Technology (ONT) was employed to profile antibiotic resistance. This strain completely assembled into a chromosome, five plasmids, and a novel 38 099 bp bacteriophage. The chromosomal genome consisted of genes oqxAB, fosA5, and bla-LEN that conferred resistance to phenicol/quinolone, fosfomycin, and beta-lactam, respectively. Plasmid AA035 conferred genes for resistance to metal and heat element subtypes, i.e., silver, copper, and tellurium. The phage was determined to be a temperate that consisted of a fosB gene and conferred resistance to fosfomycin. The temperate phage will enhance our understanding of its impact on disseminating K. variicola isolates and how it will impact disease development and antibiotic resistance mechanisms in wastewater treatment plants. This study highlights the need for ongoing genomic epidemiology surveillance of environmental K. varricola isolates as well as temperate phages.