Different livelihoods have different vulnerability risks and influences on the management of marine protected areas (MPAs). This research aimed to compare the seasonal, trend and shock livelihood vulnerability indicators (LVIs) of three dominant livelihood groups and the groups’ perceptions towards supporting MPA conservation efforts. The Anambas Archipelago MPA was selected as the study site. A total of 66 respondents from the three major groups were selected using stratified random sampling and interviewed using a questionnaire containing 14 LVIs. The responses were standardised and aggregated using functional relationships. The groups’ perceptions were determined using frequency distribution and thematic analyses (NVIVO 10). The LVI composite values showed that fishers were the most vulnerable (0.65), followed by fish farmers (0.62) and ecotourism operators (0.47). Fishers and fish farmers expressed high vulnerability due to their dependency on the coastal resources. The ecotourism operators had low vulnerability due to their lower dependency on natural resources, smaller impacts from seasonal weather, low involvement in resource conflicts and greater political support. The three groups supported the MPA regimes despite differences in their knowledge of the MPA restrictions on their livelihood practices. The study’s findings provide key alternative strategies to address the vulnerability risks of the three major groups and to increase their support for conservation goals in similar MPAs.