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¹ Department of Wildlife and Fisheries, Mississippi State University, Mississippi State, MS 39762, USA DOI : 10.4194/trjfas.2009.0208 Viewed : 4120 - Downloaded : 2911 This paper assessed whether the habitat structure of the Santa Teresa lagoons, Humacao Natural Reserve (HNR), Puerto Rico was able to support long-term fisheries of tarpon (Megalops atlanticus) and common snook (Centropomus undecimalis). Relations between fish and invertebrate communities and the physicochemical and habitat structure of the lagoon system were identified. Santa Teresa 2 (ST2) was physicochemically and structurally different than Santa Teresa 1 (ST1). Reduced turbidity and increased habitat complexity created by submersed vegetation in ST2 were reflected in the composition of the fisheries resources. Tarpon predominated in ST2 and common snook predominated in ST1. Catch-perunit- effort (CPUE) of tilapia (Mozambique tilapia Oreochromis mossambicus and redbreast tilapia Tilapia rendalli) was the highest in ST2, and CPUE of grass shrimp (Palaemonetes sp.) was the highest in ST1. Tilapia represented 96% of the tarpon diet, whereas grass shrimp represented 23% of the snook diet. Links between fish habitat use and habitat structure indicated that the Santa Teresa lagoons have the habitat structure necessary to support tarpon and snook long-term fisheries. Keywords : Caribbean Sea, coastal lagoon, fisheries, habitat