Viruses of microbes are major actors across ecosystems. Here we explored the diversity of viruses infecting methanogens involved in anaerobic digestion (AD) processes. We developed an original coupling of metagenomics and stable isotope probing (SIP), to identify viruses infecting formate-assimilating methanogens during AD. 13C-labeled formate enabled to enrich and label hydrogenotrophic methanogens in batch mesophilic AD microcosms. The shotgun metagenomics of the total cellular DNA and of cellular DNA fractions obtained by separation according to mass density enabled us to generate a spacer database and a collection of Metagenome Assembled Genomes (MAGs). These were then used to identify viruses of methanogens in the shotgun metaviromes, through spacer- and signature-based approaches. The most abundant and labeled methanogens were hydrogenotrophs belonging to the genus Methanobacterium. We identified 39 viral contigs predicted to originate from viruses of methanogens. Among them, two likely originate from spindle-shaped viruses and represent two distinct new viral families. Another contig is a nearly complete genome of a caudovirus infecting Methanobacterium members and apparently also representing a new family. Consistently, spindle-shaped and head-tailed particles were observed in our samples by transmission electron microscopy. We showed the original use of DNA-SIP to identify viruses infecting key functional groups contributing to biogeochemical fluxes in communities of uncultured microbes. This significantly expanded the knowledge on the diversity of viruses of methanogens, and reinforced the notion of the widespread environmental and phylogenetic distribution of spindle-shaped archaeal viruses.