There are currently 89 recognized species in this genus: •
Melanotaenia affinis (
M. C. W. Weber, 1908) (New Guinea rainbowfish) •
Melanotaenia ajamaruensis G. R. Allen &
N. J. Cross, 1980 (Ajamaru rainbowfish) •
Melanotaenia albimarginata G. R. Allen,
Hadiaty,
Unmack &
Erdmann, 2015 (White-tip rainbowfish) •
Melanotaenia ammeri G. R. Allen,
Unmack &
Hadiaty, 2008 (Ammer's rainbowfish) •
Melanotaenia angfa G. R. Allen, 1990 (Yakati rainbowfish) •
Melanotaenia arfakensis G. R. Allen, 1990 (Arfak rainbowfish) •
Melanotaenia arguni Kadarusman,
Hadiaty &
Pouyaud, 2012 (Arguni rainbowfish) •
Melanotaenia aruensis G. R. Allen,
Hadiaty,
Unmack &
Erdmann, 2015 (Aru rainbowfish) •
Melanotaenia caerulea G. R. Allen, 1996 (Blue rainbowfish) •
Melanotaenia catherinae (
de Beaufort, 1910) (Waigeo rainbowfish) •
Melanotaenia corona G. R. Allen, 1982 (Corona rainbowfish) •
Melanotaenia duboulayi (
Castelnau, 1878) (Crimson-spotted rainbowfish) •
Melanotaenia dumasi M. C. W. Weber, 1907 (Omba rainbowfish) •
Melanotaenia etnaensis G. R. Allen,
Unmack &
Hadiaty, 2016 (Etna Bay rainbowfish) •
Melanotaenia flavipinnis G. R. Allen,
Hadiaty &
Unmack, 2014 (Misool yellowfin rainbowfish) •
Melanotaenia fluviatilis (
Castelnau, 1878) (Murray River rainbowfish) •
Melanotaenia fredericki (
Fowler, 1939) (Sorong rainbowfish) •
Melanotaenia garylangei J. A. Graf,
Herder &
Hadiaty, 2015 (Gary Lange's rainbowfish) •
Melanotaenia goldiei (
W. J. Macleay, 1883) (Goldie River rainbowfish) •
Melanotaenia gracilis G. R. Allen, 1978 (Slender rainbowfish) •
Melanotaenia grunwaldi G. R. Allen,
Unmack &
Hadiaty, 2016 (Grunwald's rainbowfish) •
Melanotaenia japenensis G. R. Allen &
N. J. Cross, 1980 (Japen rainbowfish) •
Melanotaenia kamaka G. R. Allen &
Renyaan, 1996 (Kamaka rainbowfish) •
Melanotaenia klasioensis Kadarusman,
Hadiaty &
Pouyaud, 2015 (Klasio Creek rainbowfish) •
Melanotaenia kokasensis G. R. Allen,
Unmack &
Hadiaty, 2008 (Kokas rainbowfish) •
Melanotaenia kolaensis G. R. Allen,
Hadiaty,
Unmack &
Erdmann, 2015 (Kola rainbowfish) •
Melanotaenia rubrostriata (
E. P. Ramsay &
J. D. Ogilby, 1886) (Red-striped rainbowfish) •
Melanotaenia rumberponensis Kadarusman,
Ogistira &
Pouyaud, 2015 (Rumberpon rainbowfish) •
Melanotaenia salawati Kadarusman,
Sudarto,
Slembrouck &
Pouyaud, 2011 (Salawati rainbowfish) •
Melanotaenia sembrae Kadarusman,
O. Carman &
Pouyaud, 2015 (Sembra rainbowfish) •
Melanotaenia solata W. R. Taylor, 1964 (Northern rainbowfish) •
Melanotaenia splendida (
W. K. H. Peters, 1866) •
M. s. inornata (
Castelnau, 1875) (Chequered rainbowfish) •
M. s. splendida (
W. K. H. Peters, 1866) (Eastern rainbowfish) •
M. s. tatei (
Zietz, 1896) (Desert rainbowfish) •
Melanotaenia susii Kadarusman,
Hubert &
Pouyaud, 2015 (Susi Creek rainbowfish) •
Melanotaenia trifasciata (
Rendahl, 1922) (Regal rainbowfish) •
Melanotaenia urisa Kadarusman,
Setia Wibawa &
Pouyaud, 2012 (Urisa rainbowfish) •
Melanotaenia utcheensis McGuigen, 2001 (Utchee Creek rainbowfish) •
Melanotaenia vanheurni (
M. C. W. Weber &
de Beaufort, 1922) (Van Heurn's rainbowfish) •
Melanotaenia veoliae Kadarusman,
D. Caruso &
Pouyaud, 2012 (Veolia rainbowfish) •
Melanotaenia wanoma Kadarusman,
Ségura &
Pouyaud, 2012 (Wanoma rainbowfish) •
Melanotaenia wisloni Hammer, Allen, Martin, Adams & Unmack, 2019 (little rainbowfish) •
Melanotaenia wokamensis G. R. Allen,
Hadiaty,
Unmack &
Erdmann, 2015 (Wokam rainbowfish) ==Undescribed species==