Coastal and marine natural capital stocks provide a bundle of ecosystem services vital to humans. The delivery of these benefits depends on the protection and sustainable management of natural capital through effective nature conservation strategies. Marine Protected Areas (MPAs) are recognized worldwide as important tools to protect biodiversity while ensuring the delivery of ecosystem services and promoting sustainable human activities. Following the results of a national project aimed at assessing the value of natural capital in the Italian MPAs, in this study we assessed the value of marine natural capital stocks in the Gulf of Naples and Campania Region (Southern Italy) based on a biophysical and trophodynamic accounting model. The assessment focused on four macro-habitats: sciaphilic hard bottom (SHB), photophilic hard bottom (PHB), soft bottom (SB), and Posidonia oceanica seagrass bed (PSB). The total biophysical value of natural capital stocks related to the total area of the Gulf of Naples and Campania Region was 5.70⋅1020 sej and 3.10⋅1021 sej, while the total economic value was 795.92 and 4323.16 M€. Although the SHB habitat only represents about 4% and 1% of the total marine area of the Gulf of Naples and Campania Region, it contributes by 28% and 7% to the total value of natural capital. These figures reflect the high convergence of natural input flows into the marine ecosystem for the generation of the SHB habitat, highlighting the importance of proper measures and actions for its protection. In addition, the calculated values of natural capital stocks were combined with the bionomic map of the Gulf of Naples and Campania Region to show the spatial distribution of natural capital value. The outcomes of this study can support local managers and policy makers in charge for implementing nature conservation strategies aimed at ensuring the sustainable use of marine resources.