Contemporary efforts to conserve and restore the marine environment are centred on regulating anthropogenic activities in defined ocean areas through marine protected areas (MPAs). This spatially explicit approach is contingent upon a good understanding of the biology and distribution of species. However, our understanding of many rare and threatened benthic species, for which conservation MPAs are currently being designated, is poor. The fan mussel, Atrina fragilis (Pennant 1777), a rare and vulnerable sessile benthic species that shows a reduced distribution compared to historical accounts, was used as a case species. Identifying the larvae of sessile benthic species is an essential first step in informing their conservation. Here, the first description of larva belonging to A. fragilis is presented along with key life-history traits. A point process modelling framework appropriate for the analysis of presence-only data, along with techniques to address both observer bias and uncertainties with historical occurrence records, were employed to successfully predict the distribution of A. fragilis, revealing potentially important drivers in its current distribution. The transport of A. fragilis larva, taking into account key aspects of life-history, habitat suitability and fine scale hydrodynamics, was modelled to investigate potential levels of connectivity within the Scottish sea area, allowing the potential supply of larvae to areas of suitable habitat and the Scottish MPA network to be evaluated. To date there has been no consideration of the likely effectiveness of measures in most inshore MPAs. Here we assessed the siting of MPAs in relation to fishing intensity and seabed ruggedness on the west coast of Scotland. The results suggest little reduction in fishing pressure is effected by current restrictions on activity in the subset of MPAs investigated, with protection principally being applied to rugged areas that may already act as natural refugia for vulnerable benthic species such as A. fragilis.