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The shells of unionid freshwater mussels are highly morphologically variable, making species identification difficult and thus hampering conservation efforts. Shell shape variation is associated with several factors, of which hydrodynamic variables are the most common. Using geometric morphometrics, shell shape was evaluated on the basis of both external (entire margin including alate processes) and internal (pallial line and positions of muscle scars and teeth) landmarks in Triplodon corrugatus, Paxyodon syrmatophorus and Prisodon obliquus. Samples of these species were collected from 2–5 sites on six rivers, which were classified as either small or large drainages, in the eastern Amazon region, Pará state, northern Brazil. Interspecific comparisons in shell shape were also made among all three species where they co-occurred. Shell shape differed significantly among individuals of the same species from different sites and, in cross-validation tests, 94–96% of mussels were correctly classified into their river of origin according to their shape. For all three species, canonical variates analysis consistently differentiated between mussels from sites in large and small rivers, with the greatest difference in shell shape occurring between large and small rivers. Mussels from the large, clear or whitewater Tapajós, Amazon and Tocantins sites had a triangular shape with prominent posterodorsal and anterior winged processes, whereas those from the small, clearwater Trombetas, Irituia and Piriá sites had a rounded shape, and lacked or had reduced dorsal winged processes. Where all three species co-occurred in the Tapajós and Trombetas sites, shell shape tended to converge. Paxyodon syrmatophorus from the Tapajós sites was most distinct, with very pronounced dorsal processes and a reduced shell disc. In all three species, most of the shell shape variation occurred in the posterodorsal winged process, posterior and ventral margins, and to a lesser degree, in the anterior winged process. The shape differences among Amazonian freshwater mussels agree with those of freshwater mussel species from other regions, characterized by wide variation in hydrodynamics. [ABSTRACT FROM AUTHOR]