After Weksler, Precequillo & Voss, 2006, with recent species from Nowak, 1991

Older phylogeny after Steppan, 1996, McKenna & Bell, 1997, and Weksler, 2003

<==o Oryzomyini Vorontsov, 1959
   |--+--o Mindomys Weksler, Precequillo & Voss, 2006 [Macruroryzomys Hershkovitz, 1948 (nomen nudum)]
   |  |  `-- M. hammondi (Thomas, 1913) Weksler, Precequillo & Voss, 2006 [Nectomys hammondi Thomas, 1913; Macruroryzomys hammondi (Thomas) Hershkovitz, 1948 (nomen nudum); Oryzomys hammondi (Thomas)]
   |  `--o †Megalomys Truessart, 1881 [taxonomic history] Pleist.-R. W.Ind., Pleist. NSA. [Santa Lucia & Martinique, extinct since 19th century]
   |     |-- †M. desmarestii
   |     `-- †M. luciae
   `--+--+--o Scolomys Anthony, 1924; R. SA.
      |  |  |-- S. melanops (ecuadorinpiikkihiiri)
      |  |  `-- S. ucayalensis
      |  `--o Zygodontomys J.A. Allen, 1897; Pleist.-R. SA., R. CA.
      |     |-- Z. brevicauda
      |     |-- Z. reigi
      |     `-- Z. brunneus
      `--+--+--o Euryoryzomys Weksler, Precequillo & Voss, 2006 [taxonomic history]
         |  |  |?- E. emmonsae (Musser et al., 1998) [taxonomic history]
         |  |  |?- E. legatus (Thomas, 1925) [taxonomic history]
         |  |  |?-o E. nitidus (Thomas, 1884) [taxonomic history]
         |  |  |  |-- E. n. nitidus (Thomas, 1884)
         |  |  |  `-- E. n. boliviae (Thomas, 1901)
         |  |  |--o E. macconnelli (Thomas, 1910) [taxonomic history]
         |  |  |  |-- E. m. incertus (J.A. Allen, 1913)
         |  |  |  |-- E. m. mureliae (J.A. Allen, 1915)
         |  |  |  `-- E. m. macconnelli (Thomas, 1910)
         |  |  `--+-- E. lamia (Thomas, 1901) [taxonomic history]
         |  |     `--o E. russatus (Wagner, 1848) [taxonomic history]
         |  |        |-- E. r. physodes (Brants, 1827)
         |  |        |-- E. r. intermedius (Leche, 1886)
         |  |        |-- E. r. coronatus (Winge, 1887)
         |  |        |-- E. r. kelloggi (Ávila-Pires, 1959)
         |  |        |-- E. r. moojeni (Ávila-Pires, 1959)
         |  |        `-- E. r. russatus (Wagner, 1848)
         |  `--+--o Oecomys Thomas, 1906 [Oryzomys (Oecomys) Thomas, 1906] R. CA. SA.
         |     |  |?- O. cleberi
         |     |  |?- O. flavicans
         |     |  |?- O. paricola
         |     |  |?- O. phaeotis
         |     |  |?- O. rex
         |     |  |?- O. roberti
         |     |  |?- O. rutilus
         |     |  |?- O. speciosus
         |     |  |?- O. superans
         |     |  |-- O. bicolor
         |     |  `--+--+-- O. catharinae
         |     |     |  `-- O. trinitatis
         |     |     `--+-- O. concolor
         |     |        `-- O. mamorae
         |     `--+--+--o Hylaeamys Weksler, Precequillo & Voss, 2006 [taxonomic history]
         |        |  |  |?- H. acridus (Emmons & Patton, 2005 [taxonomic history]
         |        |  |  |?-o H. laticeps Lund, 1840) [taxonomic history]
         |        |  |  |  |-- H. l. saltator (Winge, 1888)
         |        |  |  |  |-- H. l. seuanezi (Weksler et al., 1999)
         |        |  |  |  `-- H. l. laticeps Lund, 1840)
         |        |  |  |?- H. oniscus (Thomas, 1904) [taxonomic history]
         |        |  |  |?- H. perenensis (J.A. Allen, 1901) [taxonomic history]
         |        |  |  |?- H. tatei (Musser et al., 1998) [taxonomic history]
         |        |  |  |--o megacephalus group [ Oryzomys megacephalus group]
         |        |  |  |  `--o H. megacephalus (Fischer, 1814) [taxonomic history]
         |        |  |  |     |-- H. m. capito (Olfers, 1818)
         |        |  |  |     |-- H. m. cephalotes (Desmarest, 1819)
         |        |  |  |     |-- H. m. velutinus (J.A. Allen & Chapman, 1893)
         |        |  |  |     |-- H. m. goeldii (Thomas, 1897)
         |        |  |  |     |-- H. m. modestus (J.A. Allen, 1899)
         |        |  |  |     `-- H. m. megacephalus (Fischer, 1814)
         |        |  |  `--o yunganus group [Oryzomys yunganus -species group]
         |        |  |     `-- H. yunganus (Thomas, 1902) [taxonomic history]
         |        |  `--+--o Transandinomys Weksler, Precequillo & Voss, 2006 [Oryzomys (in partim); Oryzomys albigularis group]
         |        |     |  |-- T. bolivarae [Oryzomys bolivarae] [incl. ]
         |        |     |  `-- T. talamancae (J.A. Allen, 1891) [Oryzomys talamancae J.A. Allen, 1891]
         |        |     `--o Nephelomys Weksler, Precequillo & Voss, 2006 [Oryzomys (in partim); Oryzomys albigularis group]
         |        |        |-- N. albigularis (Tomes, 1860) [Hesperomys albicularis Tomes, 1860]
         |        |        |-- N. auriventer (Thomas, 1899)
         |        |        |-- N. caracolus (Thomas, 1914)
         |        |        |-- N. childi (Thomas, 1895) [incl. oconnelli J.A. Allen, 1913]
         |        |        |-- N. devius (Bangs, 1902)
         |        |        |-- N. keaysi (J.A. Allen, 1900) [incl. obtusirostris J.A. Allen, 1900]
         |        |        |-- N. levipes (Thomas, 1902)
         |        |        |-- N. maculiventer (J.A. Allen, 1899)
         |        |        |-- N. meridensis (Thomas, 1894)
         |        |        |-- N. moerex (Thomas, 1914)
         |        |        |-- N. nimbosus (Anthony, 1926)
         |        |        |-- N. pectoralis (J.A. Allen, 1912)
         |        |        `-- N. pirrensis (Goldman, 1913)
         |        `--+--o Handleyomys Voss, Gomez-Laverde & Pacheco, 2002
         |           |  |-- H. fuscatus (Allen, 1912) [Aepeomys fuscatus Allen, 1912]
         |           |  `-- H. intectus (Thomas, 1921) [Oryzomys intectus]
         |           `--o “Oryzomysalfaroi group
         |              |?- “Oryzomysrhabdops
         |              |?- “Oryzomysrostratus
         |              |?- “Oryzomyssaturatior
         |              |?-o “Oryzomysmelanotis group
         |              |  `-- “Oryzomysmelanotis
         |              |-- “Oryzomysalfaroi
         |              `--+-- “Oryzomyschapmani
         |                 `-- “Oryzomysrostratus
         `--+--+--o Neacomys
            |  |  |?- N. guianae
            |  |  |?- N. pictus
            |  |  |?- N. tenuipes
            |  |  |-- N. spinosus
            |  |  `--+-- N. minutus
            |  |     `-- N. musseri
            |  `--+-- Oligoryzomys Bangs, 1900 [Oryzomys (Oligoryzomys) Bangs, 1900] Pleist.-R. SA., R. CA.
            |     `--+-- Oreoryzomys balneator (Thomas, 1900) Weksler, Precequillo & Voss, 2006 [Oryzomys balneator Thomas, 1900] [incl. hesperus Anthony, 1924]
            |        `--o Microryzomys Thomas, 1917 [incl. Thallomyscus Thomas, 1926] [Oryzomys (Microryzomys) Thomas, 1917]
            |           |-- M. minutus
            |           `?- M. altissimus
            `--+-- Eremoryzomys polius (Osgood, 1913) Weksler, Precequillo & Voss, 2006 [Oryzomys polius Osgood, 1913]
               `--+--+--o Oryzomys sensu stricto [Oryzomys palustris group]
                  |  |  |-- Oryzomys couesi
                  |  |  `--o Oryzomys palustris (suoriisirotta)
                  |  |     |-- †O. p. antillarum Thomas, 1898 [O. antillarum]
                  |  |     `-- O. p. palustris
                  |  `--+--o Pseudoryzomys Hershkovitz, 1959; Pleist.-R. SA.
                  |     |  |-- P. wavrini
                  |     |  `-- P. simplex
                  |     `--+-- †Lundomys molitor Voss & Carleton, 1993; U.Pleist.-R. SA.
                  |        `--o Holochilus Brandt, 1835 [Mus (Holochilus) Brandt, 1835; Holochyse Lesson, 1842] M.Pleist.-R. SA.
                  |           |-- †H. primigenus Steppan, 1996
                  |           `--+-- H. brasiliensis
                  |              |-- H. sciureus[ssp. => H. brasiliensis??]
                  |              |-- H. chacarius[ssp. => H. brasiliensis??]
                  |              `-- H. magnus
                  `--+-- Sooretamys angouya (Fischer, 1814) Weksler, Precequillo & Voss, 2006 [mus angouya Fischer, 1814; Oryzomys angouya (Fischer)] [incl. buccinatus Olfers, 1818; angouya Desmarest, 1819; leucogaster Wagner, 1845; ratticeps Hensel, 1872; rex Winge, 1887; paraganus Thomas, 1924; topicius Thomas, 1924]
                     `--+--o Cerradomys Weksler, Precequillo & Voss, 2006 [Hesperomys; Oryzomys (in partim); Oryzomys subflavus group]
                        |  |-- C. maracajuensis (Langguth & Bonvincino, 2002) [Oryzomys maracajuensis Langguth & Bonvincino, 2002]
                        |  |-- C. marinhus (Bonvincino, 2003) [Oryzomys marinhus Bonvincino, 2003]
                        |  |--o C. scotti (Langguth & Bonvincino, 2002) [Oryzomys scotti Langguth & Bonvincino, 2002; Oryzomys andersoni Brooks et al., 2004]
                        |  |  |-- C. s. scotti (Langguth & Bonvincino, 2002)
                        |  |  `-- C. s. andersoni (Brooks et al., 2004)
                        |  `--o C. subflavus ( Wagner, 1842) [Hesperomys subflavus Wagner, 1842; Oryzomys subflavus Wagner, 1842] [incl. Oryzomys vulpinus Lund, 1840; Oryzomys vulpinoides Schinz, 1845; Oryzomys laticeps Winge, 1888 (non Lund, 1840)]
                        |     |-- C. s. laticeps (Winge, 1888)
                        |     |-- C. s. subflavus (Wagner, 1842)
                        |     |-- C. s. vulpinus (Lund, 1840)
                        |     `-- C. s. vulpinoides (Schinz, 1845)
                        `--+--o Nesoryzomys Heller, 1904; R. W.Pac.
                           |  |-- N. darwini
                           |  |-- N. fernandinae
                           |  |-- N. indefessus
                           |  `-- N. swarthi
                           `--+--o Aegialomys Weksler, Precequillo & Voss, 2006 [Oryzomys (in partim); Oryzomys xantheolus group]
                              |  |--o A. xantheolus (Thomas, 1894) [Oryzomys xantheolus Thomas, 1894; incl. Oryzomys baroni J.A. Allen, 1892; Oryzomys ica Osgood, 1944]
                              |  |  |-- A. x. baroni (J.A. Allen, 1892)
                              |  |  |-- A. x. ica (Osgood, 1944)
                              |  |  `-- A. x. xantheolus (Thomas, 1894)
                              |  `--o A. galapagoensis (Waterhouse, 1839) [Oryzomys galapagoensis Waterhouse, 1839; incl. Oryzomys bauri J.A. Allen, 1892]
                              |     |-- †A. g. galapagoensis (Waterhouse, 1839)
                              |     `-- A. g. bauri (J.A. Allen, 1892)
                              `--+--+-- Sigmodontomys alfari J.A. Allen, 1897; R. CA. SA. [Oryzomys (Sigmodontomys)  J.A. Allen, 1897]
                                 |  `--+-- Sigmodontomys aphrastus [Oryzomys aphrastus]
                                 |     `--o Melanomys Thomas, 1902; R. CA. [Oryzomys (Melanomys) Thomas, 1902]
                                 |        |-- M. caliginosus
                                 |        |?- M. robustulus
                                 |        `?- M. zunigae
                                 `--+-- Amphinectomys savamis Malygin, Aniskin, Isaev & Milishnikov, 1994; R. SA.
                                    `--o Nectomys Peters, 1861 [incl. Cercomys F.Cuvier, 1829 (a chimera)] Pleist.-R. SA. [Oryzomys (in partim)]
                                       |-- N. squamipes
                                       |?- N. parvipes (eteläamerikanvesirotta)
                                       `?- ?N. palmipes

Oryzomyini not treated by Weksler, 2003

    Microakodontomys transitorius Hershkovitz 1993; R. SA.
    Oryzomys Baird, 1857 [Hesperomys (Oryzomys) Baird, 1857] [incl. Micronectomys Hershkovitz, 1948 (nomen nudum); Macruroryzomys Hershkovitz, 1948 (nomen nudum)] ?U.Mioc.-R. NA. Pleist.-R. SA., R. CA. W.Ind., R. Pac. (Rice rats; riisirotat)
        O. argentatus
        O. caudatus
        O. dimidiatus
        O. fulgens
        O. gorgasi
        O. melanostoma
        O. nelsoniO. pliocaenicus

Reference(s):