Responses of ecosystems to environmental changes vary greatly across habitats, organisms, and observational scales. The Quaternary fossil record of the Po Basin demonstrates that marine communities of Northern Adriatic reemerged unchanged following the most recent glaciation, which lasted ~100,000 years. The Late Pleistocene and Holocene interglacial ecosystems were both dominated by the same species, species turnover rates approximated predictions of resampling models of a homogenous system, and comparable bathymetric gradients in species composition, sample-level diversity, dominance, and specimen abundance were observed in both time intervals. The interglacial Adriatic ecosystems appear to have been impervious to natural climate change either due to their persistence during those long-term perturbations or their resilient recovery during interglacial phases of climate oscillations. In contrast, present-day communities of Northern Adriatic differ notably from their Holocene counterparts. The recent ecosystem shift stands in contrast to the long-term endurance of interglacial communities in face of climate-driven environmental changes.