Since their first use in the mid-1980s, external passive integrated transponder (PIT) tags have facilitated innovative investigations into multiple biological traits of animals. For native freshwater mussels, PIT tags are frequently used in capture-mark-recapture applications because they allow repeated, noninvasive sampling, are easy to apply, have high retention rates, and have negligible short-term effects on growth and survival. Because of these traits, resource managers and scientists are using PIT-tagged animals to estimate survival and movement of mussels associated with restoration efforts. However, consistency is limited in how PIT tags are affixed, monitored, and reported. Thus, our objectives were to (1) share our collective experiences in PIT tagging mussels across three case studies in small, medium, and large rivers and (2) propose guidelines for tagging and reporting data from PIT tag studies with native freshwater mussels to facilitate comparisons across future studies. The number of studies that have marked mussels with PIT tags has increased over the past 10 years. The ability to detect mussels using PIT tags has substantially advanced research in three areas of mussel ecology: (1) estimating vital rates (e.g., growth and survival), (2) tracking movements and behaviors of captively propagated, wild, and translocated individuals, and (3) improving our understanding of life history traits, such as reproductive timing. Each case study offers insights on tagging methods, tag loss, tag retention, and monitoring frequency across multiple species that range in conservation status from common to rare. We conclude with best-practice guidelines for placing PIT tags on freshwater mussels and a list of variables that could be reported in future studies to facilitate cross-system comparisons.