Two variants of the Neotropical mangrove species Pelliciera rhizophorae distributed along both sides of the Isthmus of Panama were detected by different colouration of the floral bracts and the size of the floral and vegetative structures. These findings raised questions concerning a possible speciation event in P. rhizophorae, for which a series of macro- and microscopic morphological traits (reproductive and vegetative structures), molecular markers from plastid DNA and climatic profiles were analyzed. Samples of P. rhizophorae were collected in three localities from the Panamanian Caribbean and Pacific coasts. The data obtained from molecular markers and morphological traits showed significant differences between the variants. The climatic profiles showed contrasting characteristics of rainfall and temperature in their habitats: variant A is found in wetter zones and variant B occupies drier zones. Evidence suggesting that a process of incipient speciation has occurred in P. rhizophorae in response to ecogeographical isolation due to climatic factors is presented. The presence of two geographically separate genetic-morphological groups, adapted to contrasting climatic conditions, will be the basis for suggesting the existence of incipient lineages in Pelliciera.