Drosophila as a potent eukaryotes of choice for an array of investigations in various fields of research in Biology and shown to be the best model system for the studies to unravel and to understand various aspects of genetic variations and its role in evolution. The nature and extent of genetic differences between individuals of the same populations, differentiation between populations of the same species and between species of a population or subgroup or a group can be evaluated at different levels namely morphological, cytogenetic, chromosomal, biochemical, behavioural and ecological studies. The present work is related to the biochemical analysis of salivary gland secretory proteins in Drosophila. This book is related to the study of Quantitative and Qualitative analysis of salivary gland secretory proteins by SDS-PAGE stained with Coomassie Brilliant Blue and PAS and alkaline phosphatase and acid phosphatase of non-denatured secretory proteins by Native PAGE and their correlation with pupation site preference in Drosophila belonging to melanogaster and ananassae subgroup of melanogaster species group, virilis and repleta group.