Marine fish populations can be vulnerable to overfishing, as a response of their life history, ecology, and socio-economic aspects. Vulnerability assessments, in this regard, can be used to support fisheries decision-making by aiding species prioritization. Assessments like Productivity–Susceptibility Analyses are well suited for multispecies fisheries, with low gear selectivity and insufficient fishery-independent and dependent data. Using this method, we assessed local vulnerability of the Galapagos grouper (‘bacalao’; Mycteroperca olfax) and compared it with other phylogenetically-related species caught in the Galapagos’ handline-fishery. Bacalao is an overfished regionally endemic fish species, characterized by low resilience, high market and cultural value and high spatial overlap with the fishery. Our results suggested that bacalao is a species of high management priority, requiring urgent measures to prevent fisheries’ collapse. In addition, if current fishing pressure persists, other related species may become threatened in the near future. We also evaluated different management scenarios using this approach. Results suggested that the inclusion of additional no-take zones in the marine reserve, comprising key nursery habitats (such as mangroves) and spawning aggregation sites, would be necessary to reduce species vulnerability and to benefit other related species. Improving enforcement and fishers’ compliance are essential to guarantee the effectiveness of these measures.