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Trochetia is a genus of six species of which five are endemic to Mauritius. Its taxonomic classification has been changed from the Sterculiaceae family to Malvaceae recently. Molecular and morphological characterizations were carried out for the five Trochetia spp. RAPD technique was used as a molecular tool for assessing the genetic diversity of the Trochetia spp. which generated high levels of polymorphism. Both molecular and morphological data were cladistically analyzed using the UPGMA based on Jaccard's coefficient. Cluster analysis revealed two different phylogenies of Trochetia for the two different markers used. T.triflora was found to be in a closer relationship to D.mauritiana, compared to its congeneric species based on morphological characters. However, the molecular characters quite interestingly separated the genus Trochetia as a different clade from outgroups; D.mauritiana and H.genevii. Resourceful in phylogenetic methods, this work provides an understanding on the basic concepts and methods for inference of phylogeny and may serve as groundwork for further analysis of the phylogenetic relationship of Trochetia spp. and hence elucidate also on the family placement.