Fisheries professionals charged with managing muskellunge (Esox masquinongy) frequently seek population information that requires the ability to identify cohorts as well as individuals; hence, reliable tagging methods are needed. Our approach was to simultaneously assess multiple marking techniques on different life stages of muskellunge over short and long time scales. We evaluated the short‐term detection of visible implant elastomer (VIE) and passive integrated transponder (PIT) tags in muskellunge fingerlings in experimental ponds. We compared survival (relative to that of control fish) and tag retention for two PIT tagging locations (the cheek and dorsal musculature) and one VIE location (the jaw). Overwinter survival did not differ between tagged and untagged fish (84–98%), but overwinter PIT tag retention was lower for the cheek (92%) than the dorsal musculature (100%). We also fin‐clipped and VIE‐tagged (jaw) 1,651 muskellunge fingerlings from 1997 to 2002 to evaluate long‐term tag retention in a broodstock lake. In addition, 125 adult muskellunge were captured and PIT‐tagged from 2003 to 2006. Muskellunge were sampled annually with trap nets and electrofishing during spring and fall. Only 2 VIE tags were detected in adults marked as fingerlings. The proportion of PIT‐tagged adults recaptured ranged from 52% to 84% during the sampling period. Our results indicate that both VIE and PIT tags are viable short‐term marks for muskellunge fingerlings, while PIT tags appear to be reliable long‐term tags when implanted in the dorsal musculature of adults.