Publisher Summary This chapter discusses simple probabilistic models for genome shuffling introduced by Sankoff and Goldstein and applies them to the assessment of relationships among a number of bacterial genomes. In the simplest model of random genome shuffling, it is assumed that the genome consists of n fragments, linearly disposed. These fragments may consist of genes, entire operons, or other larger or smaller regions of the genome. In the absence of evidence to the contrary, it is assumed that each of these fragments has the same probability per unit time of being transposed elsewhere in the genome, even for genomes of very different sizes. The shuffling of the relative positions of the markers in one organism with respect to the corresponding markers in the other reflects the genomic history of transposition. There are a number of problems associated with the use of these kinds of data. The most serious has to do with the comparability of the different databases.