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At Ocean Drilling Program (ODP) Site 1090 on the Agulhas Ridge (subantarctic South Atlantic) benthic foraminiferal stable isotope records span the late Oligocene through the early Miocene (25–16 Ma) at a temporal resolution of ∼10 kyr. In the same time interval a magnetic polarity stratigraphy can be unequivocally correlated to the geomagnetic polarity timescale (GPTS), thereby providing secure correlation of the isotope record to the GPTS. On the basis of the isotope‐magnetostratigraphic correlation we provide refined age calibration of established oxygen isotope events Mi1 through Mi2 as well as several other distinctive isotope events. Our data suggest that the δ 18 O maximum commonly associated with the Oligocene/Miocene (O/M) boundary falls within C6Cn.2r (23.86 Ma). The δ 13 C maximum coincides, within the temporal resolution of our record, with C6Cn.2n/r boundary and hence to the O/M boundary. Comparison of the stable isotope record from ODP Site 1090 to the orbitally tuned stable isotope record from ODP Site 929 across the O/M boundary shows that variability in the two records is very similar and can be correlated at and below the O/M boundary. Site 1090 stable isotope records also provide the first deep Southern Ocean end‐member for reconstructions of circulation patterns and late Oligocene to early Miocene climate change. Comparison to previously published records suggests that basin to basin carbon isotope gradients were small or nonexistent and are inconclusive with respect to the direction of deep water flow. Oxygen isotope gradients between sites suggest that the deep Southern Ocean was cold in comparison to the North Atlantic, Indian, and the Pacific Oceans. Dominance of cold Southern Component Deep Water at Site 1090, at least until 17 Ma, suggests that relatively cold circumpolar climatic conditions prevailed during the late Oligocene and early Miocene. We believe that a relatively cold Southern Ocean reflects unrestricted circumpolar flow through the Drake Passage in agreement with bathymetric reconstructions.