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The contributions of eustasy and tectonics to the development of stratigraphic sequences are commonly hard to discern, and this has been a controversial topic that is still being debated. New data are therefore necessary to improve our understanding of the factors that govern sedimentary cyclicity. Data from the subsiding Venice and the uplifting Crotone areas in Italy allow the recognition of the different effects of Late Quaternary glacio-eustatic changes and regional tectonics on sequence architecture at different temporal scales. Shallow-marine small-scale sequences linked to short-term glacio-eustatic changes at the scale of the marine isotope substage cyclicity (10000 years) show features that developed irrespective of the local conditions of subsidence or uplift, such as a modest thickness, a similar organization of facies and thin transgressive deposits. In contrast, lower frequency composite sequences at the scale of 100000 years show strongly different architectures and stacking patterns depending on the regional tectonic context: downstepping in uplifting areas and aggradational in subsiding areas. The present results, therefore, highlight that only the architecture of small-scale sequences showing a periodicity of about 20 and 40 ka appears to be dominated by the glacio-eustatic variable, because of the very high rates of sea-level change characterizing the substage cyclicity, which overprints the regional tectonic signal.