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Citrobacter werkmanii (C. werkmanii), an opportunistic urinary bacterium that causes diarrhea, is poorly understood. Our research focuses on genetic features that are crucial to disease development, such as pathogenic interactions, antibiotic resistance, virulence genes and genetic variation. Following its morphological, biochemical, and molecular identification, the whole genome of C. werkmanii strain NIB003 was sequenced in Bangladesh for the first time. Despite having around 80% whole genome conservation, the research shows that the Bangladeshi strain forms a separate phylogenetic cluster. This emphasises the genetic variability within C. werkmanii, resulting in particular modifications at the strain level and changes in its ability to cause disease. The results of the genetic diversity analysis indicate that the Bangladeshi sequenced genome is more diverse than the other strains due to the existence of unique features, such as the presence of t-RNA binding domain and N-6 adenine-specific DNA methylases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)