Regulated gene expression is achieved in large part by controlling the activities of essential, multi-subunit RNA polymerase transcription elongation complexes (TECs). The extreme stability required of TECs to processively transcribe large genomic regions necessitates robust mechanisms to terminate transcription. Efficient transcription termination is particularly critical for gene-dense bacterial and archaeal genomes 1 - 3 wherein continued transcription would necessarily transcribe immediately adjacent genes, result in conflicts between the transcription and replication apparatuses 4 - 6 and the coupling of transcription and translation 7 , 8 would permit loading of ribosomes onto aberrant transcripts. Only select sequences or transcription termination factors can disrupt the otherwise extremely stable TEC and we demonstrate that one of the last universally conserved archaeal proteins with unknown biological function is the Factor that terminates transcription in Archaea (FttA). FttA resolves the dichotomy of a prokaryotic gene structure (operons and polarity) and eukaryotic molecular homology (general transcription apparatus) observed in Archaea. This missing-link between prokaryotic and eukaryotic transcription regulation provides the most parsimonious link to the evolution of the processing activities involved in RNA 3’-end formation in Eukarya.