- Melanotaenia affinis, North New Guinea Rainbowfish
- Melanotaenia ajamaruensis, Ajamaru Lakes Rainbowfish
- Melanotaenia angfa, Yakati Rainbowfish
- Melanotaenia arfakensis, Arfak Rainbowfish
- Melanotaenia australis, Western Rainbowfish
- Melanotaenia batanta, Batanta Rainbowfish
- Melanotaenia boesemani, Boesemans Rainbowfish
- Melanotaenia caerulea, Blue Rainbowfish
- Melanotaenia catherinae, Waigeo Rainbowfish
- Melanotaenia corona, Corona Rainbowfish
- Melanotaenia duboulayi, Crimsonspotted Rainbowfish
- Melanotaenia eachamensis, Lake Eacham Rainbowfish
- Melanotaenia exquisita, Exquisite Rainbowfish
- Melanotaenia fluviatilis, Murray River Rainbowfish
- Melanotaenia fredericki, Sorong Rainbowfish
- Melanotaenia goldiei, Goldie River Rainbowfish
- Melanotaenia gracilis, Slender Rainbowfish
- Melanotaenia herbertaxelrodi, Lake Tebera Rainbowfish
| - Melanotaenia irianjaya, Irian Jaya Rainbowfish
- Melanotaenia iris, Strickland Rainbowfish
- Melanotaenia japenensis, Yapen Rainbowfish
- Melanotaenia kamaka, Kamaka Rainbowfish
- Melanotaenia lacustris, Lake Kutubu Rainbowfish
- Melanotaenia lakamora, Lakamora Rainbowfish
- Melanotaenia maccullochi, McCulloch' s Rainbowfish
- Melanotaenia maylandi, Maylands Rainbowfish
- Melanotaenia misoolensis, Misool Rainbowfish
- Melanotaenia monticola, Mountain Rainbowfish
- Melanotaenia mubiensis, Mubi Rainbowfish
- Melanotaenia nigrans, Blackbanded Rainbowfish
- Melanotaenia ogilbyi, Ogilbys Rainbowfish
- Melanotaenia oktediensis, Oktedi Rainbowfish
- Melanotaenia papuae, Papuan Rainbowfish
- Melanotaenia parkinsoni, Parkinsons Rainbowfish
- Melanotaenia parva, Lake Kuromai Rainbowfish
- Melanotaenia pierucciae, Pieruccis Rainbowfish
| - Melanotaenia pimaensis, Pima River Rainbowfish
- Melanotaenia praecox, Dwarf Rainbowfish
- Melanotaenia pygmaea, Pygmy Rainbowfish
- Melanotaenia rubripinnis, Red-finned Rainbowfish
- Melanotaenia sexlineata, Fly River Rainbowfish
- Melanotaenia solata, Northern Rainbowfish
- Melanotaenia splendida, Eastern Rainbowfish
- Melanotaenia splendida_australis, Western Rainbowfish
- Melanotaenia splendida_inornata, Checkered Rainbowfish
- Melanotaenia splendida_rubrostriata, Red-striped Rainbowfish
- Melanotaenia splendida_splendida, Eastern Rainbow Fish
- Melanotaenia splendida_tatei, Desert Rainbowfish
- Melanotaenia sylvatica
- Melanotaenia trifasciata, Banded Rainbowfish
- Melanotaenia utcheensis, Utchee Rainbowfish
- Melanotaenia vanheurni, Van Heurns Rainbowfish
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