Flower bud dormancy in temperate fruit tree species, such as almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures that flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements (CRs) to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different CRs and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by quantitative real-time PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.