In gymnosperms, such as conifers, reproductive structures emerge from distinct shoot meristems, giving rise to pollen- or seed cones—a clear distinction from angiosperms. Dispite this fundamental difference, shared genetic mechanisms regulating female organ identity have been studied mainly through evolutionary and developmental studies. This challenge necessitates comparative approaches, often relying on known angiosperm genes. Addressing this gap, we employ Visium technology to explore the development of female reproductive structures in Norway spruce (Picea abies). Our method scrutinizes wild-type female cone primordia and vegetative shoots, highlighting pivotal pathways involved in female reproduction. The inclusion of the early cone-setting acrocona mutant enables the study of the transition from vegetative to female identity, revealing key pathways in the process.