Citrobacter rodentium is a mouse-restricted pathogen that has long been used as an in vivo model for two important human intestinal pathogen enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC). And yet, in contrast to E. coli, little is known about the bacteriophages (phages) -bacterial viruses -that infect C. rodentium, reflecting in part a need to isolate and compare phages associated with this bacterial species. Here, we isolated two novel virulent phages CrRp3 and CrRp10 that infect C. rodentium and conduct in vitro and comparative genomic studies with other, related phages. We show that CrRp3 should be considered as a new species within the genus Sp6virus in the family Podoviridae, having relatively close relations to E. coli phages K1-E and K1-5 in both gene content and genome organization. By contrast, CrRp10 genome is 98% identical to that of E. coli phage Ime09 and thus should be considered as a new strain of the latter phage. We provide evidence that genomes of CrRp3 and CrRp10 have been shaped by both horizontal genetic exchange and genetic drift. Furthermore, phylogenetic analyses showed that these phages are more closely related to E. coli phages than to those infecting members of the Citrobacter genus, suggesting that CrRp3 and CrRp10 may have evolved from E. coli phages following a host-switch event.