We have previously demonstrated that genes within experimentally characterized operons of Escherichia coli are conserved together in other genomes more frequently than genes at the borders of transcription units. Here we expand the analyses and show that, as the phylogenetic distance of the genomes compared increases, the genes remaining together must belong to genes associated into operons in other prokaryotes regardless of the operon organization of the corresponding orthologous gene pair of E. coli. At the same time, we show that the observed tendencies of genes within operons to keep very short inter-genic distances in E. coli, is the same in any other prokaryote whose genome is currently available. We also show the relationship between our analyses of conservation and the inference of functional relationships from genomic context.