The specific name "perla", used as a noun in apposition, simultaneously refers to the pearly white bar-colouring on the body and to the Pearl Islands, where the three type specimens were collected.

[2] The blennies are primarily brown and yellow in colour, also displaying the aforementioned white stripes.

[2] P. perla shares the radiating lines in its eyes with its sister species P. bicirrus and P. punctata, a trait Hastings describes as being possibly unique to members of Protemblemaria.

[2] Hastings theorizes that Protemblemaria perla is most closely related to its southern Caribbean sister taxon P.

[2] The full extent of the distribution of Protemblemaria perla is uncertain, as it is only known from two male and a single female specimen collected from Isla del Rey, Pearl Islands, Panama, in the eastern central Pacific Ocean.