The McMurdo Dry Valleys possess a cold and dry climate which favours biomolecular preservation, and present the possibility for preservation of biological materials over long timescales. We examined patterns of bacterial DNA abundance and diversity in algal mats from 8–26 539 years of age. Bacterial DNA abundance was inferred from extractable DNA quantity and quantitative polymerase chain reaction targeting the bacterial 16S rRNA gene. Because damage to bacterial DNA could limit its availability for polymerase chain reaction, the efficacy of DNA repair by a commercially available kit was also examined. Polymerase chain reaction amplicons of the bacterial 16S rRNA gene were obtained from seven of eight samples. Bulk DNA abundance and bacterial 16S rRNA gene copy number of template DNA declined with increasing sample age consistent with expectations of accumulation of DNA damage in ancient materials. Clone libraries revealed age related patterns of abundance for some bacterial phylogenetic groups. For example, Firmicutes and several other lineages were abundant in ancient samples, but Cyanobacteria were absent. This points to a biased persistence of bacterial lineages that change over time since photosynthesis was active.