Abstract We have devised a procedure for the inter-species comparison of transcriptomic data and used this to reconstruct the expression dynamics of major genetic modules that were present at least 149 million years ago in the most recent common ancestor (MRCA) of living angiosperms. We begin by using Laser-Assisted Microdissection to generate novel transcriptomic data from female flower tissues of Amborella trichopoda, the likely sister to all other living angiosperms. We then employ a gene-expression clustering method, followed by a custom procedure to compare genetic modules on the basis of gene-orthology between Amborella and the molecular-genetic model angiosperm Arabidopsis thaliana (Arabidopsis). Using this protocol, we have succeeded in identifying nine major genetic modules that appear to have conserved their expression dynamics from an early stage in angiosperm evolution. The genes of these modules, representing over 5000 orthogroups, include around a third of those known to control female reproductive development in Arabidopsis. Our study constitutes a proof-of-concept for the comparison of transcriptomic data between widely diverged plant species and represents a first step in the large-scale analysis of gene expression dynamics in a macro-evolutionary context.