We use survival analysis to compare failure of passive integrated transponder (PIT) tags and loss of metal ear tags in 2,277 southern flying squirrels (Glaucomys volans), 124 house mice (Mus musculus), 112 hispid cotton rats (Sigmodon hispidus), and 374 deer (Peromyscus maniculatus) and cotton mice (P. gossypinus). With the exception of cotton rats, failure rates between ear and PIT tags differed by species. Flying squirrels exhibited the highest proportional loss of both tag types and lost ear tags more readily than PIT tags failed. The opposite was true for cotton rats and deer and cotton mice. Most PIT tags appeared to fail shortly after implantation (≤3 days), except for flying squirrels and, to a lesser extent, cotton rats. Ear tags exhibited a consistent rate of loss in flying squirrels. Body mass did not influence failure of PIT tags; however, flying squirrel body mass was associated with increased loss of ear tags. For flying squirrels PIT tag failure increased with the number of times an individual had already received a PIT tag that failed. We provide recommendations for using PIT and ear tags in marking rodents based on species-specific patterns and suggest the combined use of external and internal markers to obtain the most reliable estimates of population parameters.