Groucho is a co-repressor that interacts with many transcription factors playing a crucial role in animal development. The evolutionary origins of Groucho are not clear. It is generally regarded as being a distinct animal specific protein, although with similarities to the yeast Tup-like proteins. Here I show that Groucho has true orthologs in unicellular relatives of animals. Based on their phylogenetic distribution, and an analysis of ligand binding residues, these genes are unlikely to be orthologs of the fungal Tup-like genes. By identifying conserved candidate Groucho interaction motifs in non-metazoan transcription factors, I demonstrate that the details of molecular interactions between Groucho and transcription factors are likely to have been established prior to the origin of animals, but that the association of Groucho interaction motifs with many transcription factor types can be regarded as a metazoan innovation.