Historical evidence suggests that the Vulnerable Mediterranean monk seal Monachus monachus, one of the most threatened pinniped species, commonly used to haul out on open beaches. However, in recent times, probably driven by increased human disturbance, the species tends to seek refuge in remote marine caves, typically those that include one or more entrances above or below water level, an entrance corridor, an internal pool, and a beach that provides a dry haul-out area. Here we present evidence of monk seals using a bubble cave, an air-filled chamber or dome, accessible through an underwater passage, where seals remain in the water without any platform or beach to haul out. These wet, less accessible and inconspicuous domes may not only provide refuge against human disturbance but also play a role as resting sites, complementing breeding and haul-out caves. The observations reported here suggest that habitat suitability studies for the Mediterranean monk seal may benefit from including bubble caves, as they provide valuable resting spots, especially in tourist areas where seals may be exposed to human disturbance.