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In non-thermoregulating and sessile organisms, such as the imperiled freshwater mussels (Bivalvia: Unionida), thermal sensitivity of mitochondria is a key factor for survival to global warming. Given the protected status of many unionids, non-destructive biopsies and subsequent cryopreservation are advisable procedures for further investigation of their mitochondrial function. To address whether long-term cryopreservation affects mitochondria in freshwater mussels, the mitochondrial respiration in permeabilized somatic cells of Elliptio complanata has been fully characterized through high-resolution respirometry. Our results indicate that cryopreservation does affect the absolute rate of respiration, which significantly decrease compared to fresh tissues, independently of substrates combination, respiratory state and normalizing factor. However, the negative impact is not reflected at the level of flux control ratios, suggesting that, even in front of a sharp decline in the aerobic capacity, cryopreserved tissues preserve the mitochondrial organization and could be thus employed for the qualitative analysis of mitochondrial function.