Circadian rhythms are perhaps among the genetically best characterised behaviours. Several mutations with drastic effects on circadian processes have been identified and models developed to explain how clock genes and their products generate self-sustained oscillations. While natural variations in circadian phenotypes have been studied extensively, the genetic basis of such adaptive variations remains largely unknown. Here we report the results of a preliminary genetic analysis of adaptive divergence of circadian phenotypes in populations of fruit flies Drosophila melanogaster. Two sets of populations- early and late were created in a long-term laboratory selection for morning and evening emergence with four independent replicates each. Over the course of ~55 generations, the early flies evolved increased morning emergence and shorter circadian period, while late flies evolved increased evening emergence and longer period. To examine the genetic basis of circadian phenotypes, we set-up crosses between early and late flies and monitored emergence and activity/rest rhythms in the F1, backcrossed and F2 progeny. Our analysis suggests that the genetic basis of divergent circadian phenotypes in early and late stocks is primarily autosomal. Line-cross analysis revealed that additive and non-additive genetic effects contribute to the divergence of circadian phenotypes in early and late flies.