Abstract Biochemical processes associated with the interactions of acidophilic and pressure-adapted thermophilic or thermoadapted microorganisms suitable for enhanced oil recovery produce characteristic chemical markers. These markers indicate the extent and the nature of chemical alterations of crude oils by microorganisms which have been experimentally introduced and grown in crude oils. The chemical markers include high and low molecular-weight species, organic sulfur compounds, trace metals, and the extent of emulsification. Most recent results suggest that the distribution of major groups of compounds, i.e., the asphaltenes, maltenes, and saturates are also biochemically altered. Experimental evidence indicates that multiple biochemical reactions are involved in the microbial interactions with crude oils. The chemical markers associated with these biochemical reactions are described and discussed in terms of their significance and applicability to the biotreatment of crude oils and enhanced oil recovery.