The species Rotala pusilla was described in 1856 by Louis René Tulasne. He based it on plants found in Madagascar.
According to the Rotala revision by C.D.K. Cook (1979), R. pusilla is a synonym of the very variable, almost worldwide species Rotala mexicana.
The aquarium plant Rotala mexicana 'Araguaia', which is said to originate from Brazil (Rio Araguaia), also came into the trade under the name Rotala pusilla. For this reason R. pusilla is given here as a synonym of R. mexicana 'Araguaia', although it is actually a synonym of the entire species R. mexicana and not only of the local form 'Araguaia'.