BackgroundProteus mirabilisis a Gram-negative bacteria most noted for its involvement with catheter-associated urinary tract infections. It is also known for its multicellular migration over solid surfaces, referred to as ‘swarming motility’. Here we analyzed the genomic sequences of twoP. mirabilisisolates, designated K38 and K39, which exhibit varied swarming ability.Methods and resultsThe isolates genomes were sequenced using Illumina NextSeq sequencer, resulting in about 3.94 Mbp, with a GC content of 38.6%, genomes. Genomes were subjected for in silico comparative investigation. We revealed that, despite a difference in swarming motility, the isolates showed high genomic relatedness (up to 100% ANI similarity), suggesting that one of the isolates probably originated from the other.ConclusionsThe genomic sequences will allow us to investigate the mechanism driving this intriguing phenotypic heterogeneity between closely relatedP. mirabilisisolates. Phenotypic heterogeneity is an adaptive strategy of bacterial cells to several environmental pressures. It is also an important factor related to their pathogenesis. Therefore, the availability of these genomic sequences will facilitate studies that focus on the host–pathogen interactions during catheter-associated urinary tract infections.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11033-023-08518-x.