Science currently recognises 18 species of pencilfish, all in the single genus – Nannostomus.
| Nannostomus anduzei | Anduzi’s pencilfish |
| Nannostomus beckfordi | Beckford’s pencilfish |
| Nannostomus bifasciatus | Whiteside pencilfish |
| Nannostomus britskii | Spotstripe pencilfish |
| Nannostomus digrammus | Two stripe pencilfish |
| Nannostomus eques | Brown pencilfish |
| Nannostomus espei | Barred pencilfish |
| Nannostomus grandis | Great pencilfish |
| Nannostomus harrisoni | Blackstripe pencilfish |
| Nannostomus limatus | Elegant pencilfish |
| Nannostomus marginatus | Dwarf pencilfish |
| Nannostomus marilynae | Greenstripe pencilfish |
| Nannostomus minimus | Least pencilfish |
| Nannostomus mortenthaleri | Coral red pencilfish |
| Nannostomus nitidus | Shining pencilfish |
| Nannostomus rubrocaudatus | Red-tailed pencilfish |
| Nannostomus trifasciatus | Threestripe pencilfish |
| Nannostomus unifasciatus | Oneline pencilfish |
Nannostomus 