The identity of this name is not clear. The type collection was cited in the protologue as deposited at F and Cooper & Slater 53. A collection corresponding to this number has only been located as a specimen at US that is a species of Annonaceae. There is a specimen of Cooper & Slater 50 at US that is Pentagonia and has a number of details that agree with the protologue description of the type of Pentagonia bocataurensis, including being from Bocas del Toro and having an annotation as Pentagonia magnifica. Because of these confused points, it has been postulated that Cooper & Slater 50 is likely the intended type collection of Pentagonia bocataurensis (M. Grayum, pers. comm.). However, the locality for Cooper & Slater 50 is Almirante, not the locality given by Dwyer, Changuinola. No complete specimen of Cooper & Slater 53 or 50 has been found currently at F (F. Barrie, pers. comm., 2021), although a Pentagonia specimen there is labelled as Cooper 50 and anonymously identified as Pentagonia magnifica has been located there; this specimen comprises a single leaf.
The protologue description of Pentagonia bocataurensis lacks some clarifying details, such as petiole length, pubescence, and size of the bracts, but it does have flower details so it clearly is associated with some flowering specimen. Dwyer contrasted Pentagonia bocataurensis in the protologue with Pentagonia magnifica, but the details he cited for the latter are inaccurate. This name was overlooked by Lorence (1999), and was considered of unclear identity in Flora Mesoamerica.
The type collection of Pentagonia bocataurensis was apparently cited inaccurately, but no specimen has been located that is likely the intended specimen unless it is the specimen of Cooper & Slater 50 in US. At present this possiblity cannot be confirmed without further review of F specimens. Based on the protologue description, this species may not be distinct from Pentagonia nuciformis, described in the same work, or Pentagonia wendlandii.