Understanding the potential future impacts of climate change along the supply chain for highly traded fisheries products can inform choices to enhance future global seafood security. We examine the supply chains of the Australian tropical rock lobster fishery (TRL) and southern rock lobster fishery (SRL), with similar destination markets but different catch methods and fishing communities. A boat-to-market analysis allows for comparison and illustration of the effects of single supply-chain aspects. We used life cycle assessment to provide an overview of the environmental footprint, expressed as global warming potential (GWP), eutrophication, and cumulative energy demand, for two lobster products: live animals and frozen tails. The export phase contributed 44% and 56% of GWP of live-weight lobster for SRL and TRL, respectively. The SRL fishery currently produces 68% of the combined 1,806.7 tonnes of lobster product and 78% of the combined global warming for the two fisheries over the whole supply chain. We develop climate adaptation options that: (1) reduce the overall footprint; (2) consider alternative supply-chain strategies (e.g., reduce cost); and (3) predicted impact of future climate change. Adaptation options include: more direct export routes and change in the export transport mode. Value adding and product differentiation, which can level out seasonality and thus spread risk, is likely to become increasingly important for both increases and decreases in predicted climate-induced abundance of fish species.