Sediments from the Tasman Basin in the southwest Pacific Ocean show a cyclic pattern of variation in mineral magnetic properties, including susceptibility and remanence, over the Brunhes Chron. The magnetic pattern is dominated by fluctuations in the concentration of a single domain ferrimagnetic component identified as bacterial magnetofossils by TEM investigation of the magnetic fraction. The intervals of low bacterial magnetite concentration, occurring in glacial periods, are accompanied by a change of the bacterial magnetosome morphology assemblage interpreted as recording a change in bacterial species assemblage. There is no evidence of iron or sulphate reducing conditions during low bacterial magnetite intervals. Concentrations of bacterial magnetite are low when oxygen concentrations in surface sediment pore waters dropped, either as the result of variation in bottom water oxygen concentration or sedimentation rate. The variations in the magnetic signal are therefore interpreted as resulting primarily from bacterial palaeoecological control rather than dissolution or alteration. The bacteria in this deep sea environment are apparently aerophilic and grow near the sediment surface within the oxic zone, implying that magnetic remanence is also acquired near the surface but up to tens of centimetres below where the oxic zone is very thick.