The unsaturation ratio of C(37) alkenones (U(37)(K')) produced by haptophyte microalgae such as Emiliania huxleyi is often used as proxy for past sea surface temperature. In this study, 29 bacterial strains were isolated from cultures of the strain E. huxleyi TWP1. Among alkenone-degrading isolates, the strain Dietzia maris sp. S1 appeared to be able to selectively degrade alkenones leading to increases in the palaeoenvironmental proxy U(37)(K') by +0.05 to +0.10 units, which is equivalent to the change seen when the growth temperature is increased by 1.5-3.0 degrees C. This degradation was shown to involve initial epoxidation of the alkenone double bonds presumably by a monooxygenase, which showed a preference for oxidation of the omega29 double bond. Inconsistencies observed in previous studies of the aerobic microbial degradation of alkenones may simply reflect which species of bacteria were present. Our results confirm that intense aerobic bacterial degradative processes can introduce a bias in palaeotemperature reconstructions especially when there is evidence of substantial aerobic bacterial degradation of the deposited organic matter. The widespread occurrence of epoxyalkenones in the marine environment strongly suggests that selective aerobic bacterial degradation could be major source of uncertainty for palaeotemperature estimation.