The structures of three distant Proteus mirabilis populations were studied, according to a standard fingerprinting analyses and a different types of marker (dispersed, repetitive) sequences. The relative values of resultant dendrograms topology parameters were applied for comparative analysis. The established correspondences suggest analogous mechanisms leading to strain differentiation in each of the investigated group of strains. It has been shown that the marker sequence may be assigned to phenetic UPGMA dendrogram structure, independently on bacterial population, and therefore may be applied as a marker of the population structure itself. The interpretation of two parameters of UPGMA tree has been proposed. The averaged node number, calculated along the homology axis, may be applied as a measure of species genome  homogeneity/uniformity, while its standard deviation may be referred as the homogeneity tolerance. It has been pointed out that appropriately defined series of dendrogram parameter relative values may be valuable for building up an individual species genome characteristics. Additionally, the concept of ‘dispersed locus’ referring to the set of neighbourhoods/surroundings of a marker target sequence, as a tool for describing species genome flexibility, has been formulated. Experimentally measured P. mirabilis species genome relative uniformity is slightest in the set neighbourhoods of enterobacterial repetitive consensus sequences (ERIC), and the highest in neighbourhoods of repetitive BOX sequence. The regions neighbouring the analysed microsatellite tandem repeats represent the medium position. Certain parameter combinations allowed to create, via Ward’s minimal variance analysis, separate clusters which were congruent with the applied marker type.