Genetic control of the timing of flowering in woody plants is complex and has yet to be adequately investigated due to their long life-cycle and difficulties in genetic modification. Studies in Populus, one of the best woody plant models, have revealed a highly conserved genetic network for flowering timing in annuals. However, traits like continuous flowering cannot be addressed with Populus. Roses and strawberries have relatively small, diploid genomes and feature enormous natural variation. With the development of new genetic populations and genomic tools, roses and strawberries have become good models for studying the molecular mechanisms underpinning the regulation of flowering in woody plants. Here, we review findings on the molecular and genetic factors controlling continuous flowering in roses and woodland strawberries. Natural variation at TFL1 orthologous genes inboth roses and strawberries seems be the key plausible factor that regulates continuous flowering. However, recent efforts suggest that a two-recessive-loci model may explain the controlling of continuous flowering in roses. We propose that epigenetic factors, including non-coding RNAs or chromatin-related factors, might also play a role. Insights into the genetic control of flowering time variation in roses should benefit the development of new germplasm for woody crops and shed light on the molecular genetic bases for the production and maintenance of plant biodiversity.