Although association of circadian clock properties with the timing of rhythmic behaviors (chronotype) has been extensively documented over several decades, recent studies on mice and Drosophila have failed to observe such associations. In addition, studies on human populations that examined effects of clock gene mutations/polymorphisms on chronotypes have revealed disparate and often contradictory results, thereby highlighting the need for a suitable model organism to study circadian clocks’ role in chronotype regulation, the lack of which has hindered exploration of the underlying molecular-genetic bases. We used a laboratory selection approach to raise populations of Drosophila melanogaster that emerge in the morning ( early) or in the evening ( late), and over 14 years of continued selection, we report clear divergence of their circadian phenotypes. We also assessed the molecular correlates of early and late emergence chronotypes and report significant divergence in transcriptional regulation, including the mean phase, amplitude and levels of period ( per), timeless ( tim), clock ( clk) and vrille ( vri) messenger RNA (mRNA) expression. Corroborating some of the previously reported light-sensitivity and oscillator network coupling differences between the early and the late populations, we also report differences in mRNA expression of the circadian photoreceptor cryptochrome ( cry) and in the mean phase, amplitude and levels of the neuropeptide pigment-dispersing factor (PDF). These results provide the first-ever direct evidence for divergent evolution of molecular circadian clocks in response to selection imposed on an overt rhythmic behavior and highlight early and late populations as potential models for chronotype studies by providing a preliminary groundwork for further exploration of molecular-genetic correlates underlying circadian clock-chronotype association.