Distributions of oxygen in surface sediments from central Sagami Bay were quantified using an autonomous vehicle carrying both a profiling microelectrode instrument and a planar optode module. Measurements were performed at 16 sites (either by microelectrodes or optodes) along a ∼175m long transect and in total 45 electrode microprofiles and 6 O2 images (each covering 6.9×5.1cm of surface sediment) were obtained. The data revealed an extensive small-scale variation of the in situ O2 distribution. The diffusive O2 uptake (DOU) as derived from the microelectrode data varied by a factor >10 with an average value of 2.6±1.6mmolm−2 d−1 ( n = 45 ) corresponding to ∼8% of the estimated average primary production for the area. There was no significant difference in the average O2 penetration depth as quantified from the microprofiles and the planar optode images ( P < 0.05 ). The O2 penetration depth of the combined dataset varied between 0.5 and 9.2mm with an average value of 3.9±1.5mm ( n = 347 ). Even though the organic carbon rich sediments of central Sagami Bay may exhibit higher horizontal heterogeneity than normally encountered in deep-sea sediments, the data document that extrapolation from a few in situ data points should be done with caution. A detailed statistical analysis of the spatial autocorrelation in the O2 penetration depth documented that measurements performed less than 2cm apart were autocorrelated. This implies that the aerobic benthic activity at the investigated site varied in patches with a characteristic size of a few cm. The presented data represent a detailed in situ study on small-scale spatial variability in sediment O2 distribution and document that planar O2 optode images provide a tool to access spatial heterogeneity of natural sediments.