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Data-limitations increase the uncertainty of quantitative ecosystem models and have the potential to slow the progress of Ecosystem Based Fisheries Management. However, the most important finding of perturbation analysis for managers is arguably simple trends in community abundance. Qualitative models can be used to predict trends following perturbation and require only the signs (+, -, 0) of interactions between variables. To further increase the utility of qualitative models in ecosystem analysis, complementary alternative models, with differing uncertainties and assumptions can be used to assess the robustness of conclusions. Qualitative models and an Ecopath with Ecosim model were produced to investigate the inshore reef ecosystem of eastern Tasmania, Australia. The impact of fisheries, competition between fish species, and increasing urchin abundance on ecosystem dynamics were investigated. Qualitative models highlighted the need to decrease fisheries catches, the potential for cascading effects due to urchin grazing, and the capacity for large rock lobster to allow the regeneration of foliose algae. Ecopath with Ecosim produced consistent conclusions for the majority of qualitative predictions. Inconsistent conclusions were discussed with regard to differences in model calculation and behavior. The process undertaken in this study may allow progress in ecosystem analyses in data-poor situations, which may aid the development and implementation of Ecosystem Based Fisheries Management.