The molecular regulation of induction and development of reproductive organs is well established in angiosperms, while it is slowly accumulating in gymnosperms. Here, we conducted comparative transcriptomic profiles at different stages of male and female cone development in Pinus halepensis. Our aim was to reveal transcription factor encoding genes involved in reproductive induction and development. For accurate developmental stage identification, histological analysis preceded the molecular analysis. The flowering induction genes FT/TFL were expressed mainly at the late developmental stages of the male cone, suggesting involvement in vegetative bud dormancy instead of flowering induction. The male cone development was associated with the expression of the C-class PhMADS2, and the B-class genes PhDAL11 and PhDAL13, while the female cone development was associated with the expression of the C-class MADS1 and DAL14 genes. This study adds valuable knowledge to the profile of transcription factors and MADS-box genes regulating cone development in gymnosperms.