Abstract Archaea use eukaryotic-like DNA replication proteins to duplicate circular chromosomes similar to those of bacteria. Although archaeal replication origins have been maintained during the evolution, they are non-essential under laboratory conditions. Here we propose the local deviations from Chargaff’s second parity rule of archaeal chromosomes result from the biased gene orientation and not from mutational biases. Our computational and experimental analyses indicate that the archaeal replication origins prevent head-to-head collisions of replication and transcription complexes as well as participate in coordination of the transfer of genetic information. Our results therefore suggest that the archaeal replication origins have alternative functions not related to their role in initiation of DNA replication.