Sport fisheries for muskellunge (Esox masquinongy) are often sustained by stocking. Size‐selective mortality has been identified as an important factor affecting stocked muskellunge, However, this mortality is difficult to assess because its effects on the population can be confounded by growth. To partition observed shifts in length frequencies of stocked muskellunge into growth and mortality effects, two lots each of approximately 1,000 hatchery‐reared muskellunge fingerlings were sorted into 10‐mm size‐groups, marked with size‐specific fin clips, and stocked into two northwestern Wisconsin lakes. Beginning 30 d after stocking, we used electrofishing to examine length distributions and estimate abundance of stocked fish. Shifts in the length‐frequency distributions after stocking were found to be caused by size‐selective mortality and growth. Mortality was highest for the smallest fish. A size‐based analysis indicated that growth in fall contributed far more than size‐selective mortality contributed to changes in length distributions. Our analysis suggests that it may be important to monitor the fate of size‐classes within cohorts if cohort dynamics are to be fully understood.