| | Family | Species | GenBank accession number | | 16S rDNA | 18S rDNA |
| | Acestrorhynchidae | Acestrorhynchus abbreviatus | FJ944707 | FJ944764 | | Acestrorhynchus microlepis | FJ944708, FJ944709 | FJ944765, FJ944766 |
| | Anostomidae | Leporinus fasciatus | FJ944710 | FJ944767 | | Leporinus muyscorum | FJ944711 | FJ944768 | | Rhytiodus microlepis | FJ944712 | FJ944769 | | Schizodon fasciatus | FJ944713 | FJ944770 |
| | Chalceidae | Chalceus erythrurus | FJ944723 | FJ944779 |
| | Characidae | Astyanax abramis | FJ944714 | FJ944771 | | Astyanax aff. fasciatus | FJ944715 | FJ944772 | | Astyanax magdalenae | FJ944716 | FJ944773 | | Astyanax microlepis | FJ944717 | FJ944774 | | Brycon amazonicus | FJ944718 | FJ944775 | | Brycon cephalus | FJ944719 | FJ944776 | | Brycon henni | FJ944720 | FJ944777 | | Bryconops melanurus | FJ944721, FJ944722 | FJ944778 | | Charax michaeli | FJ944724 | FJ944780 | | Charax tectifer | FJ944725 | FJ944781 | | Ctenobrycon hauxwellianus | FJ944726 | FJ944782 | | Cynopotamus magdalenae | FJ944727 | FJ944783 | | Hemibrycon boquiae | FJ944728 | FJ944784 | | Hemibrycon dentatus | FJ944729 | FJ944785 | | Moenkhausia comma | FJ944730 | FJ944786 | | Moenkhausia lepidura | FJ944731 | FJ944787 | | Moenkhausia melogramma | FJ944732 | FJ944788 | | Roeboides myersii | FJ944733 | FJ944789 | | Stethaprion erythrops | FJ944734 | FJ944790 | | Tetragonopterus argenteus | FJ944735 | FJ944791 | | Triportheus albus | FJ944736 | FJ944792 | | Triportheus angulatus | FJ944737 | FJ944793 | | Triportheus magdalenae | FJ944738 | FJ944794 |
| | Ctenoluciidae | Boulengerella maculata | FJ944739 | FJ944795 | | Ctenolucius hujeta | FJ944740 | FJ944796 |
| | Curimatidae | Curimatopsis macrolepis | FJ944741 | FJ944797 | | Cyphocharax magdalenae | FJ944742 | FJ944798 | | Potamorhina altamazonica | FJ944743 | FJ944799 | | Potamorhina latior | FJ944744 | FJ944800 | | Psectrogaster amazonica | FJ944745 | FJ944801 | | Psectrogaster rhomboides | FJ944746 | FJ944802 | | Psectrogaster rutiloides | FJ944747 | FJ944803 | | Steindachnerina guentheri | FJ944748 | FJ944804 | | Steindachnerina hypostoma | FJ944749 | FJ944805 |
| | Cynodontidae | Hydrolycus scomberoides | FJ944750 | FJ944806 | | Rhaphiodon vulpinus | FJ944751 | FJ944807 |
| | Gasteropelecidae | Carnegiella strigata | FJ944752 | FJ944808 | | Thoracocharax stellatus | FJ944753 | FJ944809 |
| | Prochilodontidae | Prochilodus magdalenae | FJ944754 | FJ944810 | | Prochilodus nigricans | FJ944755 | FJ944811 | | Semaprochilodus insignis | FJ944756 | FJ944812 |
| | Serrasalmidae | Colossoma macropomum | FJ944757 | FJ944813 | | Mylossoma aureum | FJ944758 | FJ944814 | | Mylossoma duriventre | FJ944759, FJ944760 | FJ944815 | | Pygocentrus nattereri | FJ944761 | FJ944816 | | Serrasalmus elongatus | FJ944762 | FJ944817 | | Serrasalmus rhombeus | FJ944763 | FJ944818 |
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