The protection of the Vulnerable Marine Ecosystem identified by the presence of the critically endangered bamboo coral Isidella elongata has been recognized as an urgent task. Although some research has focused on its spatial distribution, there is no available information on this species connectivity and genetic structure. This study aims to investigate, for the first time, the genetic diversity pattern and the inter-population connectivity of I. elongata at the Mediterranean scale. A DNA-based approach was used to assess the genetic diversity of 33 I. elongata samples collected in six different areas using two mitochondrial genes (COI and MutS), and a nuclear one (ITS2). Molecular results confirmed that all samples belonged to I. elongata and showed a scarce level of intra- and inter-populational mtDNA differentiation, whereas nuDNA data showed higher genetic structuring. Furthermore, a Lagrangian model (forward-in-time simulations) was used to investigate the species larval connectivity under different sea currents conditions. Our results suggest the presence of persistent pathways, supporting the self-sustaining nature of the populations, especially in the central Mediterranean Sea. This study finding are discussed in light of the implementation of management measures encompassing both the conservation of vulnerable species and the sustainability of deep-water fisheries.