The life histories of organisms, including growth and reproduction, are closely linked to seasonality. Phenology, the temporal coordination of biological activities, such as leaf flushing and flowering in plants, is governed by gene expression dynamics in response to seasonal environments. However, the mechanisms underlying the evolution of seasonal gene expression remain unclear. In this study, we compared genome-wide expression dynamics under natural seasonal conditions (molecular phenology) in four dominant evergreen Fagaceae species (Quercus glauca, Q. acuta, Lithocarpus edulis, and L. glaber), using leaf and bud tissues over two seasonal cycles. We first assembled high-quality reference genomes for Q. glauca and L. edulis and identified 11749 single-copy orthologous genes. Seasonal transcriptomic profiling revealed highly conserved gene expression across species in winter, particularly in buds, when temperatures fall below ~10°C. Rhythmic gene expression was detected more frequently in buds (51.9%) than leaves (40.6%), with the majority of rhythmic genes (78.4–92.0%) displaying annual periodicity, while only a small fraction (1.2–11.9%) showed half-annual cycles. The seasonal peaks of rhythmic genes were highly synchronized across species in winter but diverged during the growing season, aligning with key phenological events such as leaf flushing and flowering. Genes with conserved seasonal peaks exhibited slower protein coding-sequence evolutionary rates, suggesting weak selective pressures maintaining seasonal gene expression, while the evolutionary rates were similarly slow regardless of whether genes were expressed in winter or the growing season. These findings suggest that winter gene expression is more conserved than that in the growing season, imposing a seasonal constraint on the evolution of gene expression. This constraint may restrict temporal niche partitioning and potentially slow species divergence rates in seasonal environments.