Nondestructive tissue sampling is desirable for genetic or physiological studies of endangered freshwater mussels. We used the freshwater pearl mussel (Margaritifera margaritifera) to evaluate 4 sampling methods (haemolymph extraction, foot scraping, mantle biopsy, and viscera swabbing) with regard to their effectiveness for deoxyribonucleic acid (DNA) analyses and their effects on sampled mussels. One hundred twenty-eight days subsequent to tissue sampling (1 June–7 October), all sampled individuals were alive, and average growth of sampled individuals was not significantly different from unsampled, control individuals, except that the viscera-swabbing group had lower growth. The magnitude of decreased growth in viscera-swabbed individuals was small (∼0.5 mm less than controls), and the biological significance of this result is unclear. DNA yields from haemolymph extraction and foot scraping were significantly lower and more variable than yields from the other methods. Genotyping success was lowest for haemolymph extraction and mantle biopsy, but was high for the other methods. Viscera-swab samples stored in lysis buffer at room temperature prior to DNA extraction had higher DNA yield than samples stored in buffer at 4°C or samples stored dry, but genotyping success was equivalent among storage methods. On the basis of these results, we recommend use of the noninvasive viscera-swabbing method.