Summary It is well established that micro‐organisms colonize a variety of extreme environments, including habitats like oil reservoirs deep inside the earth crust. Here, we present the results of a comparative high‐coverage DNA sequencing study of metagenomes derived from two different oil reservoirs, both located about 2.5 km subseafloor below the Norwegian Sea. A previously reported bioinformatic analysis of DNA sequence data derived from one of the reservoirs (Well I) indicated that the community is dominated by bacterial species with a smaller fraction of Archaea. Here, we report results of a similar analysis from another reservoir (Well II) located in the same geographical area, however, according to available geological knowledge lacking direct physical contact with Well I. Interestingly, the Well II community is largely dominated by Archaea with a subordinate fraction of Bacteria. Comparison of the two datasets showed that large fractions of the sequences are extremely similar, both with respect to identity (typically above 98%) and gene organization. We therefore conclude that both wells contain essentially the same organisms, but in different relative abundances. Assuming that the communities have been distinct for long timescales because of physical separation, the results also indicate that microbial growth in the reservoirs is extremely slow.