- Enneapterygius abeli, Yellow Triplefin
- Enneapterygius altipinnis, Highfin Triplefin
- Enneapterygius atriceps, Hawaiian Blackhead Triplefin
- Enneapterygius atrogulare, Ringscale Threefin
- Enneapterygius bahasa, Blacktail Threefin
- Enneapterygius bichrous, Northern Bicoloured Triplefin
- Enneapterygius cheni
- Enneapterygius clarkae, Barred Triplefin
- Enneapterygius clea, Clea' s Threefin
- Enneapterygius destai
- Enneapterygius elegans, Elegant Threefin
- Enneapterygius etheostoma
- Enneapterygius fasciatus
- Enneapterygius flavoccipitis, Two-colour Threefin
- Enneapterygius fuscoventer, Blackbelly Triplefin
- Enneapterygius gracilis, Yellow-black Threefin
- Enneapterygius hemimelas, Halfblack Threefin
- Enneapterygius hollemani, Hollemans Triplefin
| - Enneapterygius howensis, Lord Howe Threefin
- Enneapterygius kermadecensis, Kermadec Triplefin
- Enneapterygius larsonae, Blackhead Threefin
- Enneapterygius melanospilus
- Enneapterygius minutus, Minute Triplefin
- Enneapterygius mirabilis, Miracle Threefin
- Enneapterygius miyakensis, Izu Islands Triplefin
- Enneapterygius namarrgon, Lightning-man Threefin
- Enneapterygius nanus, Pygmy Threefin
- Enneapterygius nasimae, Pakistan Triplefin
- Enneapterygius niger, New Caledonian Black Triplefin
- Enneapterygius nigricauda, Pacific Blacktail Triplefin
- Enneapterygius obscurus
- Enneapterygius ornatus, Henderson Triplefin
- Enneapterygius pallidoserialis, Pale White-spotted Triplefin
- Enneapterygius paucifasciatus, New Caledonian Striped Triplefin
- Enneapterygius philippinus, Minute Threefin
- Enneapterygius pusillus, Highcrest Triplefin
| - Enneapterygius pyramis, Pyramid Threefin
- Enneapterygius randalli, Rapa Triplefin
- Enneapterygius rhabdotus, South Pacific Striped Triplefin
- Enneapterygius rhothion, New Caledonian Blackhead Surf Triplefin
- Enneapterygius rubicauda, Redtail Triplefin
- Enneapterygius rufopileus, Blackcheek Threefin
- Enneapterygius signicauda, Flagtail Triplefin
- Enneapterygius similis, Masked Threefin
- Enneapterygius triserialis, Whitespotted Threefin
- Enneapterygius trisignatus
- Enneapterygius tutuilae, Highfin Threefin
- Enneapterygius unimaculatus, Onespot Triplefin
- Enneapterygius ventermaculus, Blotched Triplefin
- Enneapterygius vexillarius, Blacksaddle Triplefin
- Enneapterygius williamsi, Williams Triplefin
- Enneapterygius ziegleri, Ziegler' s Threefin
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