I have been completely enamored of pencil fish for some time now, and with the new shipments I have been getting in from Peru, have only become more so. I have gotten in three species of pencil so far, Nannostomus mortenthaleri, Nannostomus rubrocaudatus, and Nannostomus marginatus.
To the casual observer, these fish are very easy to confuse with one another but there are a few ways you can tell them apart.
Nannostomus mortenthaleri (Coral Red) is my favorite of the three. It was originally classified as a cf. marginatus, but was distinguished and has some notable characteristics which help to determine its species. There is a pronounced sexual dimorphism where the males are extremely bright red between the central and upper dark lateral stripes, from the tip of their nose to the base of the caudal fin. All three of their lateral strips are distinctive, but their dorsal fin has all rays partially black and the edge of the pelvic and anal fin is black. The dorsal fin also has a white spot at the base, on males, with a red tip. As with all the Nannostomus, they lack an adipose fin.
Nannostomus rubrocaudatus (purple pencil fish) are quite similar, but with a few notable differences, color being the easiest way to distinguish them from mortenthaleri. Purple pencil males have a much more purple coloration in the rear half of the body, and the color is more uniform. Also, the ventral fins are reddish and lack the white blotch which the coral red pencils have.
Lastly, Nannostomus marginatus (Dwarf Pencil) are easiest to confuse with non-dominant or female Purple Pencils, but can be distinguished as their body lacks all red pigmentation, other than a small red stripe above the central dark stripe. They sometimes will have a yellow pigmentation to their body and fins.