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For fruit tree species, bud endodormancy is a crucial step, as its progression over winter determines the quality of blooming and the flowering time. Understanding the relationship between endodormancy, ecodormancy, and flowering processes is thus a fundamental goal in molecular biology studies of these species mainly in the present climate change and warming context. Knowing the molecular basis of the control of endodormancy and flowering will allow us to develop efficient selection tools like molecular markers for monitoring the process. In this 2-year study, to understand the transcriptional changes leading to the endodormancy release of flower buds, we cloned a candidate transcript and analysed its expression by qPCR in the flower buds of three almond (Prunus dulcis (Miller) Webb) cultivars with different endodormancy period lengths and flowering times. The candidate transcript, named PdP40, has been described as a member of the flower-specific class III peroxidase family. Expression results highlight a significant increase in the transcript levels of this gene before endodormancy release in the three cultivars assayed, independent of the endodormancy period. Furthermore, total peroxidase activity was analysed in flower bud samples. Results suggest an important role for this peroxidase in this process and the possibility of using it as an expression marker for predicting endodormancy release in the field.