Ribonucleoside monophosphates (rNMPs) are the main non-canonical nucleotides in genomic DNA, and their incorporation can occur as mismatches or matches in vivo. To counteract the mutagenic potential of rNMPs in DNA, all organisms evolved ribonucleotide excision repair (RER), a mechanism initiated by type 2 RNase H. Here, we describe the in vitro reconstitution of matched and mismatched rNMP repair using archaeal RER enzymes. Our data suggest two types of RER pathways, including the classical flap RER and a back-up RER with the order of reactions changed for Fen1 and Pols. The genomic rNMP level in RER-deficient or PolB-deficient archaeal cells along with in vitro reconstitution of RER suggest an in vivo role of PolD in RER. Our results provide insights into how matched and mismatched rNMPs may be processed by RER.