Rapid warming of the Mediterranean Sea threatens marine biodiversity, particularly key ecosystems already stressed by other impacts such as Posidonia oceanica meadows. A 6-year monitoring of seawater temperature and annual P. oceanica shoot demography at Cabrera Archipelago National Park (Balearic Islands, Western Mediterranean) allowed us to determine if warming influenced shoot mortality and recruitment rates of seagrasses growing in relative pristine environments. The average annual maximum temperature for 2002–2006 was 1 °C above temperatures recorded in 1988–1999 (26.6 °C), two heat waves impacted the region (with seawater warming up to 28.83 °C in 2003 and to 28.54 °C in 2006) and the cumulative temperature anomaly, above the 1988–1999 mean annual maximum temperature, during the growing season (i.e. degree-days) ranged between 0 °C in 2002 and 70 °C in 2003. Median annual P. oceanica shoot mortality rates varied from 0.067 year−1 in 2002 to 0.123 year−1 in 2003, and exceeded recruitment rates in all stations and years except in shallow stations for year 2004. Interannual fluctuations in shoot recruitment were independent of seawater warming (P>0.05). P. oceanica meadows experienced a decline throughout the study period at an average rate of −0.050±0.020 year−1. Interannual variability in P. oceanica shoot mortality was coupled (R2>0.40) to seawater warming variability and increasing water depth: shoot mortality rates increased by 0.022 year−1 (i.e. an additional 2% year−1) for each additional degree of annual maximum temperature and by 0.001 year−1 (i.e. 0.1% year−1) for each accumulated degree water temperature remained above 26.6 °C during the growing season. These results demonstrate that P. oceanica meadows are highly vulnerable to warming, which can induce steep declines in shoot abundance as well indicating that climate change poses a significant threat to this important habitat.