The family Drosophilidae consists over described about 4,000 species. Molecular characterization and comparison among different species of Drosophilidae (Diptera) is necessary for the study of the divergence pattern in Drosophilidae. To understand the phylogenetic relationship among the species of the family Drosophilidae, RAPD polymorphic patterns were analyzed from the species of Drosophilidae. Four random primers have been used for present study. The degree of relatedness among the species was studied by cluster analysis and multidimensional scaling and also by Jaccard similarity coefficient analysis. This book provides the molecular phylogenetic tree of the species of Drosophilidae. The phylogenetic tree, generated by RAPD analysis, is in nearly complete congruence with the classification based on morphophenotypic characters.This book also gives a clear idea about the relationship of indian Drosophilidae with the other members of this family.