Climate changes are expected to induce significant modifications in biodiversity on the global scale, but little is known as to how biodiversity has been affected by recent changes in the deep sea. We have used nematodes to investigate the response of deep-sea biodiversity to an extensive climate anomaly that modified the physico-chemical characteristics of the deep waters of the Eastern Mediterranean. Using a decadal data set (from 1989 to 1998), we provide evidence that deep-sea nematode diversity can be strongly and rapidly affected by temperature shifts. The abrupt decrease in temperature (of about 0.4 °C) and modified physico-chemical conditions that occurred between 1992 and 1994 caused a significant decrease in nematode abundance and a significant increase in diversity. This temperature decrease also resulted in decreased functional diversity and species evenness, and in an increase in the similarity to colder deep-Atlantic fauna. When the temperature recovered (after 1994–1995), the biodiversity only partially returned to previous values. We conclude that deep-sea fauna is highly vulnerable to environmental alteration, and that deep-sea biodiversity is also significantly affected by very small temperature changes. The results presented here provide new elements towards a better understanding of the potential large-scale consequences of climate change.