The present study shows new evidence of morphological traits that supports the hypothesis of diversification between two genetic variants of Pelliciera rhizophorae (Tetrameristaceae), the most ancient species in the Neotropical mangrove ecosystem. Previous studies using molecular markers identified two variants of this species. Our new study, using pollen grain morphology, revealed differences in pollen sculpture between the two variants; that is, in Variant A the exine is characterised as perforate—verrucose, while in Variant B, it is punctuate. Pollen size in Variant A is larger than in Variant B, whereas the exine is thicker in Variant B than in Variant A. The differences in pollen morphology between the two variants represent new evidence suggesting that a diversification process might be occurring within P. rhizophorae, possibly due to adaptive processes in response to environmental conditions or pollination vectors.