Sweden and Finland have chosen locations for high-level radioactive waste repositories (HLRW). In the process, they have constructed underground research laboratories (URL). The Swedish URL is named Äspö Hard Rock Laboratory and is situated on the South East coast of Sweden about 400 km south of Stockholm. The Finnish URL is named ONKALO and is located in the Olkiluoto area on the west coast of Finland, about 200 km north of Helsinki. Both URLs reach about 450 m underground and are excavated in crystalline, plutonic bedrock. The sites have been investigated thoroughly for microbiology over a period of about 20 years. The main difference between the sites is that in ONKALO there are large amounts of methane below about 300 m depth that can reach up to 1000 mL methane or more per liter of groundwater at 800 - 1000 m, while the Äspö groundwater typically has amounts of methane in the 0.1 - 5 mL L-1 range. Äspö groundwater is rich in sulphate and sulphate reducing bacteria down to 450 m but not deeper, while ONKALO groundwater is almost free from sulphate and SRB at depths below 350 m. Although both URLs are situated in similar geological hard rock settings, their geochemical characteristics are very different. In this work, a total of 12 samples from ONKALO (8 groundwater and 4 biofilms) and 6 from Äspö (6 groundwater) were successfully sequenced to a total of 326 000 reads.