This study marks the first identification and genomic characterization of Comamonas kerstersii isolates from diarrheal patients in Bangladesh. C. kerstersii is a gram-negative opportunistic bacterium that has also been reported in several clinical samples, including urine, blood, stool, peritoneal liquid, and sputum. We carried out the whole genome sequencing of three C. kerstersii isolates with the aim of analyzing genomic features in 3 different strains isolated from Bangladesh for the first time. Phylogenetic analysis suggests that these three strains share a clonal relationship. Seven AMR genes, aph(6)-Id, aph(3”)-Ib, mph(E), mph(F), msr(E), sul2, and tet(A), have been observed in all the strains. We identified several virulence factors, including copper homeostasis genes, type IV pili, and type VI secretion system. Phage regions and IncQ1 plasmid were also detected. These initial findings highlight the need for extensive genomic surveillance of C. kerstersii in different diarrheal patients, along with investigating their genotype-phenotype correlation to understand the molecular pathogenesis in detail.