The dataset includes 360 records with 236 carbon and nitrogen isotopic signatures of Callinectes sapidus and 224 isotopic data of potential prey gathered from five countries and 12 locations between 2014 and 2019.

The study of Stygofauna and Troglofauna is critical to preserve subterranean biodiversity and ecosystem functioning in spite of climate change. However, underground habitats, often hosting unique and endemic species, present significant challenges for traditional biodiversity assessments due to their inaccessibility and the specialised nature of their inhabitants, which results in paucity of academic studies. Furthermore, in many places knowledge of underground fauna is mainly held by non-academic site experts, such as nature guides, amateur speleological groups and environmental area managers. This valuable knowledge is rarely organised and shared according to modern data management criteria, making it less usable for research purposes. Reawakening this dormant data, standardising and sharing it according to modern criteria offers enormous opportunities to expand existing academic knowledge and provide support for future studies. This long-term dataset represents a unique and invaluable resource for elucidating the characteristics of Apulian subterranean ecosystems. Integrating observations already published in previous studies with unpublished records, this is the first complete data collection on Apulian Speleofauna organised according to modern standards of data sharing.