The name Pelargonium come from Pelargos (Greek word): meaning, stork; Stork's Bill which refers to the rostrum (beak-like extension) of the schizocarp (dry splitting fruit into two or more parts) which resembles the bill of a stork. Tongaense refers to the Tongaland area, KZN where this species was discovered.

Material of P. tongaense was originally collected in 1955 by Mr. Jobe Mafuleka (a farm-worker), and he brought the plants to Mr Ian Garland who cultivated them. Reports indicate that in October 1973, the existence of these plants was known to botanists J.J.A. Van der Walt & P.J. Vorster and they expressed some doubts as to whether the plants were indigenous or not. The climatic conditions where these plants grow naturally in Tongaland were found to be somehow uncommon for the genus Pelargonium, and was then thought these plants were perhaps hybrids from P. peltatum & P. inquinans. It was only in November 1981, when Libelepi, young son of Mr Mafuleka took the above-mentioned experts to the natural locality where P. tongaense grows, that the two were then convinced that this was a separate species and it was formally described.