Oecomys (Rodentia, Sigmodontinae, Oryzomyini) is a taxonomically complex and cytogenetically diverse genus with a controversial intraspecific phylogenetic relationship. Karyotypic analyses, using whole chromosome probes from Hylaeamys megacephalus (HME, Sigmodontinae, Oryzomyini) in some taxonomic lineages of this genus have detected the rearrangements that shaped their karyotypes, in addition to revealing relevant insights into the taxonomic status of these taxa. Thus, to investigate the chromosomal evolution of the genus, we characterized the karyotype of Oecomys rutilus (ORU) with HME probes, establishing chromosomal homology maps with the karyotypes of other congeners. The chromosomal phylogeny obtained by Maximum Parsimony analysis recovered the genus Oecomys as monophyletic, with moderate bootstrap support (68%). This clade branches into two large groups, the first including O. rutilus followed by O. catherinae-Rio de Janeiro and O. catherinae-Pará
the other group includes O. auyantepui followed by O. paricola cytotype C and O. paricola cytotype A + cytotype B. We detected that these taxa underwent intensive reorganization of their karyotypes, the rearrangements producing this diversity were 15 pericentric inversions, 12 centric fusions, 11 fissions, 5 in tandem fusions, 8 translocations and the addition/deletion of constitutive heterochromatin on two autosomes and the X chromosomes. However, despite the high number of chromosomal rearrangements found, we identified some entirely conserved syntenic blocks shared among all species analyzed. From these data, we hypothesized a putative ancestral karyotype. We also detected exclusive characteristics for ORU, the syntenic blocks HME 1/20/4 (ORU 1), HME (16,17)/3 (ORU 2), HME 2/1 (ORU 4), HME 2/7 (ORU 5), HME 5/(9,10)/8 (ORU 3), HME 19/12 (ORU 9). We provide an overview of the chromosomal reorganization of the genus that points to a high chromosomal diversity and show that chromosomal rearrangements play an important role in the radiation of these species.