Magnetostratigraphy is described for a sequence of predominantly hemipelagic marine mudstone, 2200 m thick, representing the Late Miocene and earliest Pliocene from the Mangapoike River section, eastern North Island, New Zealand. Together with the early Pliocene magnetostratigraphy previously described from Mangapoike, it now provides a 3000 m thick magnetostratographic reference section for New Zealand, ranging in age from 10.5 Ma to 3.5 Ma. Thirteen magnetozones are recognised in the 2200 m described here and all but the highest are confidently correlated with the polarity timescale from the base of Chron 11 to Chron 7. Correlation of the highest (normal) magnetozone to the timescale is ambiguous, and two possible interpretations are presented, both of which imply a previously unrecognised latest Miocene unconformity. The inferred unconformity is supported by biostratigraphy. It is shown that the integration of biostratigraphy, lithostratigraphy and magnetostratigraphy can discern diastems of the order of 10 (super 4) years. Magnetostratigraphy and delta (super 13) C data also indicates a diastem between 6.30 Ma to 5.41 Ma at the Miocene-Pliocene angular unconformity at Mangapoike. These two unconformities and a distinct lithological change at the base of the Late Miocene are synchronous with deep-sea benthic delta (super 18) O records and unconformities expected from postulated eustatic sea-level changes. A coherent correlation model for New Zealand on-shore magnetostratigraphic, biostratigraphic and isotopic data conflicts with the two magnetostratigraphic interpretations proposed for DSDP Site 594, 150 km east of New Zealand, both of which are probably incorrect.