Complete XbaI and BlnI cleavage maps of Escherichia coli K-12 strain MG1655 are presented, along with a comparison of the physical map of MG1655 with that of five other K-12 strains. We have mapped 35 XbaI cleavage sites generating 35 fragments ranging in size from 8 kb to 432 kb using methods similar to those used previously for the NotI and SfiI maps of MG1655. The applicability of the MG1655 map to other strains of E. coli K-12 was assessed by comparing the NotI, SfiI and XbaI digestion patterns of EMG2, W1485, W3110, AB1157 and MC4100 with those of MG1655. The variability between strains, some of which are separated by numerous steps of mutagenic treatment, is readily detectable by pulsed-field gel electrophoresis. A model is presented to account for the differences between the strains on the basis of simple insertions, deletions and, in one case, an inversion. Insertions and deletions ranging in size from 1 kb to 86 kb are suggested by this model. Several of the larger features have previously been characterized and some of the smaller rearrangements can potentially account for previously reported genetic features of these strains. The various features localized in these strains were used to place 9 of the 17 BlnI fragments on the E. coli physical map. The remaining fragments were placed by hybridization experiments similar to those used for the NotI, SfiI and XbaI maps. In this way, the complete BlnI map was constructed. The cleavage sites for XbaI and BlnI were assigned coordinates based on EcoMap6 developed by Rudd et al. The XbaI and BlnI maps of MG1655 presented here, when combined with the NotI (22 sites) and SfiI (31 sites) maps of MG1655 previously published, bring the total number of mapped rare restriction sites in MG1655 to 105. The strain comparison analysis shows that this map is readily adaptable for use with other K-12 strains.