Trees, like many other organisms, decrease their rate of metabolic activities to cope up with harsh environments. This stage of "dormancy" is marked by shedding of leaves and bud-set in deciduous trees. Recent studies have revealed the role of the circadian clock in synchronizing the timing of dormancy and physiology for conferring fitness in trees. To better understand the possible role of natural selection on circadian clock-related genes in climatic adaptation, I took a candidate gene approach, selecting circadian clock genes, some of which had been functionally validated, and others hypothesized, to identify signatures of natural selection in Populus trichocarpa and P. deltoides. Using both frequency spectrum based tests and tests of heterogeneity, I identified genetic variants deviating from selective neutrality. Results reveal that photoreceptors and dormancy regulator genes may have been the targets of natural selection. Nearly the same levels of selective constraints were found in different functional groups of genes irrespective of pleiotropy. Further, upstream regions of all genes showed high selective constraint, with some of them (FT-2, PIF-4, FRIGIDA) showing significantly higher variation than the other genes, hinting at the role of non-coding regulatory regions in local adaption. In some cases, the same genes in both species appeared as outliers, including PIF-6, FRI, FT-2, SRR1, TIC, and CO, which might reflect their common role in adaptation across species boundaries. All of these results indicate a complex nature of phenology regulation and local adaptation in Populus species with photoreceptors and dormancy regulator genes playing key roles.