Sulphate-reducing bacteria (SRB) and magnetotactic bacteria (MTB) are two special groups of prokaryotes that emerged early in Earth’s history. These extremotolerant bacterial groups have rarely been identified or studied within cave and karst environments, especially hyperalkaline cave systems (pH > 9), such as Poole’s Cavern in Derbyshire, England. In this study, we identify the sulphate-reducing MTB Desulfovibrio magneticus, within this hyperalkaline cave system. It appears to survive in a diverse range of environments including soil, stalactites and cave sediments. Additionally, we identify various extremotolerant SRB in similar Poole’s Cavern environments. We show that these SRB and MTB can move successfully into subsurface environments and adapt concomitantly to the anomalous pH, saline, and relatively nutrient-poor conditions found in Poole’s Cavern. These findings are significant to our understanding of microorganisms on early Earth because it is believed, but not proven, that underground environments might have been hot spots for early microbial life. We expect that these early bacteria would have been able to adopt similar adaptation strategies, transferring and acclimatizing to underground environments, in ways comparable to the SRB and MTB identified in this study.