Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P.tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10-15% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5-7% of the phenotypic variation in growth cessation.