1. Biogenic reefs formed by bivalves are biodiversity hot spots that provide important ecosystem services, but are globally endangered. In Strangford Lough (Northern Ireland) the use of mobile fishing gear (MFG) has caused extensive damage to reefs formed by the horse mussel (Modiolus modiolus L.), leading to declines in their extent and condition.
2. Captive breeding and translocation have been proposed as potential restorative strategies for the remaining reefs, and thus the reproductive biology of M. modiolus as the keystone species needs to be described prior to attempting large‐scale ecological restoration.
3. Physiological condition and gametogenesis were studied in two sympatric M. modiolus subpopulations using direct gonad assessment methods. The size‐ and age‐frequency structure of the whole metapopulation were described to establish present or past recruitment events.
4. Although gonad condition remained high in each year for the two subpopulations studied, significant losses were recorded in one subpopulation. These observations are consistent with autumn and winter spawning, but were not recorded in reefs thought to be more damaged by MFG.
5. Length‐ and age‐frequency histograms showed a distinct bimodal distribution in all remnant M. modiolus subpopulations, which were dominated by mussels over 50 years old. Little or no successful recruitment has occurred in some subpopulations, where low reproductive output caused by declines in broodstock numbers might be preventing natural recovery.
6. A combined approach of strict protection of the remaining larval sources and active restoration through stock supplementation is recommended to address recruitment limitations and increase connectivity between remnant subpopulations.