Pelliciera rhizophorae is the sole survivor of the Eocene mangroves inhabiting the Isthmus of Panama. Two populations of Pelliciera rhizophorae, a small morphotype at the Pacific coast and a tall morphotype at the Caribbean coast, display significant morphological and molecular differences. The patterns of differentiation between these two morphotypes were not determined by the isthmus itself, but are probably due to a process of adaptation in response to the climate that resulted in specific traits for the two populations. Aiming to verify if the ecological isolation also caused changes in the karyotype of the two morphotypes, we investigated the number of chromosomes, size, morphology, distribution of CMA, DAPI bands and nuclear DNA content of the Atlantic and Pacific populations of P. rhizophorae. A diploid chromosome number of 2n = 34 was found in both morphotypes, exhibiting small metacentric, submetacentric and acrocentric chromosomes. The acrocentric chromosomes presented the largest CMA+bands which are often associated with the nucleolus. Nuclear DNA content was similar in both variants (2.52 pg and 2. 56 pg for the small and tall morphotypes respectively), evidencing a small genome. Although the two morphotypes were karyotypically very similar, we observed a consistent difference in digestibility of their root tips in cellulase–pectinase solution and in the stainability of their cytoplasm. The cytotaxonomical relationship between Pelliciera and the related taxa is also discussed.