We describe a straight forward approach for determining whole genome sequence similarity of more than 30 species of Enterobacteriaceae with a focus on the genus Enterobacter and related taxa by sequence amplification and determination of the recN, rpoA and thdF genes using conserved primer binding sites as previously shown for the family Pasteurellaceae (Kuhnert & Korczak, 2006). The sequences provide valuable data for phylogenetic, taxonomic and diagnostic purposes. Sequence information on all three genes is highly representative for the species’ %GC-content. On the other side the recN sequence alone is sufficient to extrapolate whole genome similarities between species of Enterobacteriaceae. Finally, the rpoA genes sequence, which is the easiest one to determine, provides a powerful diagnostic tool to identify and differentiate important food contaminants. The comparative analysis gives important insights into the taxonomy and phylogeny of the family Enterobacteriaceae and will serve as a basis for further studies and clarifications on the taxonomy of this large and heterogeneous family.