After Armbruster, 2004, with Recent species from Froese & Pauly, 2001 [“The FishBase”]

<==o Hypostomini Kner, 1853
   |--+-- Hypostomus boulengeri (Eigenmann & Kennedy, 1903)
   |  `-- Hypostomus commersoni Valenciennes, 1836
   `--+--+--+-- Hypostomus sp. “round snout” 1
      |  |  |-- Hypostomus bolivianus (Pearson, 1924)
      |  |  `-- Hypostomus punctatus Valenciennes, 1840 [Plecostomus punctatus] (täpläimumonni, täpläpleko)
      |  `--+-- Hypostomus albopunctatus (Regan, 1908)
      |     `-- Hypostomus francisci (Lütken, 1874)
      `--+--+-- Hypostomus sp. “round snout 2”
         |  `--+-- Hypostomus plecostomus (Linnaeus, 1758) 1 [Acipenser plecostomus Linnaeus, 1758] (Suckermouth catfish)
         |     |-- Hypostomus plecostomus (Linnaeus, 1758) 1 (Suckermouth catfish)
         |     |-- Hypostomus cordovae (Günther, 1880)
         |     |--+-- Hypostomus micromaculatus Boeseman, 1968
         |     |  `-- Hypostomus robinii Valenciennes, 1840 (Teta)
         |     `--+-- Hypostomus hemicochliodon
         |        `--o Cochliodon Heckel, 1854 [Hypostomus Lacépède; Armbruster, 2004]
         |           |-- C. cochliodon (Kner, 1854)
         |           |-- C. hondae (Regan, 1912)
         |           |-- C. levis (Pearson, 1924) [Rhinelepis levis Pearson, 1924; Hypostomus levis (Pearson); Isbrücker, 1980; Cochliodon levis (Pearson); Armbruster & Page, 1997]
         |           |-- C. oculeus (Fowler, 1943)
         |           |-- C. plecostomoides Eigenmann, 1922
         |           |-- C. pospisili Schultz, 1944
         |           |-- C. pyrineusi Miranda-Ribeiro, 1920
         |           `-- C. taphorni Lilyestrom, 1984
         `--o Hypostomus emarginatus -group (Armbruster & Page, 1996, Armbruster, 1998a, and Armbruster, 2004)
            |--o Isorineloricaria Isbrücker, 1980 [Hypostomus Lacépède; Armbruster, 2004]
            |  |-- I. festae (Boulenger, 1898) (Zucchini catfish)
            |  `-- I. spinosissima (Steindachner, 1880)
            `--+-- Hypostomus emarginatus Valenciennes, 1840 1. [Squaliforma Isbrücker & Michels, 2001 (in partim)]
               `--+-- Hypostomus emarginatus Valenciennes, 1840 2. [Squaliforma Isbrücker & Michels, 2001 (in partim)]
                  |-- Hypostomus squalinus Jardine & Schomburgk, 1841 [Squaliforma Isbrücker & Michels, 2001 (in partim)]
                  `--o Aphanotorulus Isbrücker & Nijssen, 1982 [Hypostomus Lacépède; Armbruster, 2004]
                     |-- A. ammophilus Armbruster & Page, 1996
                     `-- A. unicolor (Steindachner, 1908)

The list of Hypostomus-species not treated by Armbruster (2004):

Note: Armbruster (2004) treated all Hypostomines as members of the genus Hypostomus.

    Hypostomus Lacépède, 1808 [Acipenser Linnaeus, 1758 (in partim); Cheiridodus Eigenmann, 1922; Plecostomus Gronovius, 1754; Watawata Isbrücker & Michels, 2001] (purjeimumonnit)
        H. affinis (Steindachner, 1877)
        H. agna (Miranda-Ribeiro, 1907)
        H. alatus Castelanau, 1855
        H. ancistroides (Ihering, 1911)
        H. angipinnatus (Leege, 1922)
        H. argus (Fowler, 1943)
        H. asperatus Castelnau, 1855
        H. aspilogaster (Cope, 1894)
        H. atropinnis (Eigenmann & Eigenmann, 1890)
        H. auroguttatus Kner, 1854
        H. borellii (Boulenger, 1897)
        H. brevicauda (Günther, 1864)
        H. brevis (Nichols, 1919)
        H. butantanis (Ihering, 1911)
        H. carinatus (Steindachner, 1881)
        H. carvalhoi (Miranda-Ribeiro, 1937)
        H. commersonoides (Marini, Nichols & La Monte, 1933)
        H. coppenamensis Boeseman, 1969
        H. corantijni Boeseman, 1968
        H. crassicauda Boeseman, 1968
        H. derbyi (Haseman, 1911)
        H. dlouhyi Weber, 1985
        H. fluviatilis (Schubart, 1964)
        H. garmani (Regan, 1904)
        H. goyazensis (Regan, 1908)
        H. gymnorhynchus (Norman, 1926)
        H. hemiurus (Eigenmann, 1912)
        H. hermanni (Ihering, 1905)
        H. hoplonites Rapp Py-Daniel, 1988
        H. iheringii (Regan, 1908)
        H. interruptus (Miranda-Ribeiro, 1918)
        H. isbrueckeri Reis, Weber & Malabarba, 1990
        H. jaguribensis (Fowler, 1915)
        H. johnii (Steindachner, 1877)
        H. laplatae (Eigenmann, 1907)
        H. latifrons Weber, 1986
        H. latirostris (Regan, 1904)
        H. lexi (Ihering, 1911)
        H. lima (Lütken, 1874)
        H. longiradiatus (Holly, 1929)
        H. luetkeni (Steindachner, 1877)
        H. luteomaculatus (Devincenzi, 1942)
        H. luteus (Godoy, 1980)
        H. macrophthalmus Boeseman, 1968
        H. macrops (Eigenmann & Eigenmann, 1888)
        H. margaritifer (Regan, 1908)
        H. meleagris (Marini, Nichols & La Monte, 1933)
        H. microstomus Weber, 1987
        H. myersi (Gosline, 1947)
        H. nematopterus Isbrücker & Nijssen, 1984
        H. niceforoi (Fowler, 1943)
        H. nickeriensis Boeseman, 1969
        H. niger (Marini, Nichols & La Monte, 1933)
        H. nigromaculatus (Schubart, 1964)
        H. nudiventris (Fowler, 1941)
        H. obtusirostris (Steindachner, 1907)
        H. occidentalis Boeseman, 1968
        H. panamensis (Eigenmann, 1922)
        H. pantherinus Kner, 1854
        H. papariae (Fowler, 1941)
        H. paranensis Weyenberg, 1877
        H. paucimaculatus Boeseman, 1968
        H. paulinus (Ihering, 1905)
        H. piratatu Weber, 1986
        H. pseudohemiurus Boeseman, 1968
        H. pusarum (Starks, 1913)
        H. rachovii (Regan, 1913)
        H. regani (Ihering, 1905)
        H. rondoni (Miranda-Ribeiro, 1912)
        H. roseopunctatus Reis, Weber & Malabarba, 1990
        H. saramaccensis Boeseman, 1968
        H. scabriceps (Eigenmann & Eigenmann, 1888)
        H. scaphyceps (Nichols, 1919)
        H. seminudus (Eigenmann & Eigenmann, 1888)
        H. sipaliwini Boeseman, 1968
        H. strigaticeps (Regan, 1908)
        H. subcarinatus Castelnau, 1855
        H. surinamensis Boeseman, 1968
        H. taeniatus (Regan, 1908)
        H. tapanahoniensis Boeseman, 1969
        H. ternetzi (Boulenger, 1895)
        H. tietensis (Ihering, 1905)
        H. topavae (Godoy, 1969)
        H. unae (Steindachner, 1878)
        H. uruguayensis Reis, Weber & Malabarba, 1990
        H. vaillanti (Steindachner, 1877)
        H. variipictus (Ihering, 1911)
        H. varimaculosus (Fowler, 1945)
        H. variostictus (Miranda-Ribeiro, 1912)
        H. ventromaculatus Boeseman, 1968
        H. vermicularis (Eigenmann & Eigenmann, 1888)
        H. verres Valenciennes, 1840
        H. watwata Hancock, 1828
        H. winzi (Fowler, 1945)
        H. wuchereri (Günther, 1864)
    Squaliforma Isbrücker & Michels, 2001 [Hypostomus  Lacépède; Armbruster, 2004 (in partim)]
        S. annae (Steindachner, 1881) [Hypostomus annae (Steindachner, 1881)]
        S. biseriata (Cope, 1872) [Hypostomus biseriatus (Cope, 1872)]
        S. emarginata (Valenciennes, 1840) [Hypostomus emarginatus Valenciennes, 1840]
        S. gomesi (Fowler, 1942) [Hypostomus gomesi (Fowler, 1942)]
        S. horrida (Kner, 1854) [Hypostomus horridus Kner, 1854]
        S. phrixosoma (Fowler, 1940) [Hypostomus phrixosoma (Fowler, 1940)]
        S. scopularia (Cope, 1871) [Hypostomus scopularius (Cope, 1871)]
        S. squalina (Jardine, 1841) [Hypostomus squalinus Jardine & Schomburgk, 1841]
        S. tenuicauda (Steindachner, 1878) [Hypostomus tenuicauda (Steindachner, 1878)]
        S. tenuis (Boeseman, 1968) [Hypostomus tenuis Boeseman, 1968]
        S. villarsi (Lütken, 1874) [Hypostomus villarsi (Lütken, 1874)]
        S. virescens (Cope, 1874) [Hypostomus virescens (Cope, 1874)]

Reference(s):