A study of the diversity and genetic structure of tropical rainforest trees is a major prerequisite to their conservation and management. Analysis of the genetic variation through isozyme electrophoresis is a powerful tool to achieve that purpose. The study determined the genetic relationship existing on three tropical trees found at UPHSD-LP namely, Bauhinia purpurea (Butterﬂy tree), Delonixregia (Fire tree) and Cassia fistula (Golden Shower tree) using electrophoretic isozyme analysis based on two substrates, Acid Phosphatase and Esterase. Frequency of common bands, similarity index, Rf values and genetic distance were determined among the three species. The results revealed that distinct bands were observed for Esterase while no distinct bands were noted for Acid Phosphatase. Results of similarity index and genetic distance are inversely proportional between any two of the three species. The study concludes that Delonixregia and Cassia fistula are closely related. Tis is followed by Bauhinia purpurea and Delonixregia. Bauhinia purpurea and Cassia fistula showed distant genetic relationship.