During the Arabidopsis reproductive process, the female whorl of the flower, known as the gynoecium, passes seven of the 20 floral stages during its development. In each of these seven stages, specific developmental events occur, ranging from gynoecium primordium establishment to complex tissue and organ differentiation. Studying gynoecium development is important for its role in fruit and seed formation. Currently, there are many Arabidopsis lines with fluorescent proteins that provide relevant information on gynoecium patterning. However, the fluorescence of some proteins is affected during the steps of histological techniques. Furthermore, the complexity of gynoecium development makes live imaging difficult in the early stages and medial tissues. To address these issues at hand, we describe a methodology that facilitates the analysis of the fluorescent signal during gynoecium development, using as an example the pMIR164c::VENUS line.