The timing of reproduction strongly contributes to fitness and yield in annual and perennial plants. Here, we aim to decipher molecular mechanisms and the regulatory logic that control the switch in meristem identity that occurs during floral transition, and its subsequent stabilization during inflorescence development. We use a comparative approach among annual and perennial species, including an economically important crop, to broaden the relevance of our findings and to determine the flexibility in the underlying mechanisms in different developmental contexts and in response to different environmental and endogenous signals. Floral transition is the first step in plant reproduction, it is controlled by environmental and endogenous cues, and its timing is critical to fitness in natural populations or to yield in agriculture. During floral transition the developmental identity of the shoot apical meristem and/or axillary meristems is altered causing them to switch from vegetative meristems that form leaf primordia to inflorescence meristems that produce floral primordia. This transition is a binary switch that is usually irreversible, so that after the switch the identity of the inflorescence meristem is stable and does not revert back to a vegetative meristem. We propose that a bistable-switch mechanism reinforced by feedback loops acts at the shoot meristem to control the transition, and that the switch mechanism is biased by environmental signals to allow the transition to occur. Our model proposes that APETALA2 (AP2) and APETALA2-LIKE (AP2-LIKE) transcription factors maintain the vegetative state, while the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FRUITFULL (FUL) MADS box transcription factors together with the non-coding microRNA172 (miR172) maintain the reproductive state. These two sets of factors form a mutually repressive motif that is biased from the vegetative to reproductive state by environmental cues that induce SOC1, FUL and MIR172 transcription in the shoot meristem. We propose to test this model in annual and perennial crucifer species, Arabidopsis thaliana and Arabis alpina, respectively, as well as in apple trees using state of the art transcriptomics, transgenic and genetic approaches. These experiments will form a basis for quantitative modelling of the floral transition, a crucial stage in plant development. Furthermore, we propose to identify whether there is genetic variability in the switch mechanism in apple trees in relation to the undesired alternate bearing phenomenon. This will have practical significance in manipulating reproduction patterns and yield of crops.