<p>Perennial woodland herbs in the genus <em>Thalictrum </em>exhibit high diversity of floral morphology, including four breeding and two pollination systems. Their phylogenetic position, in the early-diverging eudicots, makes them especially suitable for exploring the evolution of floral traits and the fate of gene paralogs that may have shaped the radiation of the eudicots. A current limitation in evolution of plant development studies is the lack of genetic tools for conducting functional assays in key taxa spanning the angiosperm phylogeny. We first show that virus-induced gene silencing (VIGS) of a <em>PHYTOENE DESATURASE</em> ortholog (<em>TdPDS</em>) can be achieved in <em>Thalictrum dioicum</em> with an efficiency of 42% and a survival rate of 97%, using tobacco rattle virus (TRV) vectors. The photobleached leaf phenotype of silenced plants significantly correlates with the down-regulation of endogenous <em>TdPDS</em> (P&lt;0.05), as compared to controls. Floral silencing of<em> PDS</em> was achieved in the faster flowering spring ephemeral <em>T. thalictroides</em>. In its close relative, <em>T. clavatum</em>, silencing of the floral MADS box gene <em>AGAMOUS</em> (<em>AG</em>) resulted in strong homeotic conversions of floral organs. In conclusion, we set forth our optimized protocol for VIGS by vacuum-infiltration of <em>Thalictrum</em> seedlings or dormant tubers as a reference for the research community. The three species reported here span the range of floral morphologies and pollination syndromes present in <em>Thalictrum</em>. The evidence presented on floral silencing of orthologs of the marker gene <em>PDS</em> and the floral homeotic gene <em>AG</em> will enable a comparative approach to the study of the evolution of flower development in this group.</p>