The presence of three Gomphoneis species from Chubut Province in Argentina is documented with light and scanning electron microscopy. Two of the taxa, G. patagoniana and G. eriense var. variabilis, are part of the Herculeana subgroup of Gomphoneis. Gomphoneis patagoniana is a newly discovered species and G. eriense var. variabilis is reported from Argentina for the first time. These two species have evident axial plates, differentiated apical pore fields (APFs), a stigmal opening that is round externally and slit-like internally, and areolae that are mostly triradiate in shape. The third species, G. frenguellii, is also newly discovered and described. Presence of four isolated stigmoids, undifferentiated APFs and lack of an axial plate indicates G. frenguellii is a member of the Elegans subgroup of the genus. Presence of these newly described species, and the previously unreported taxon, may also be associated with the invasive species Didymosphenia geminata. Given there is no long history of reports of Gomphoneis in the country and, in the case of G. eriense var. variabilis, its previously known distribution, it is possible that the origin of this Gomphoneis taxon is from western North America.