AbstractObjectiveHandling and tagging migrating fish might alter their behavior, limiting inference from mark–recapture studies. Posthandling flight of tributary spawning Flannelmouth Sucker Catostomus latipinnis was previously identified in Coal Creek in the upper Colorado River basin. Our objective was to determine if similar issues were present at McElmo Creek in the San Juan River basin.MethodsWe compared emigration timing of Flannelmouth Sucker that had been handled and tagged with passive integrated transponder tags during their tributary spawning run to individuals tagged in previous years and detected both entering and exiting the tributary. Linear mixed‐effects models were used to examine intrinsic and extrinsic factors contributing to exit timing.ResultSex and tagging year were associated with emigration timing, but handling did not result in posthandling flight from McElmo Creek. Females exited the tributary ~3 days before males, and larger fish emigrated earlier than smaller adults.ConclusionDifferences in capture technique and timing, available spawning habitat, and fish motivation across river systems may contribute to differences in posthandling emigration of tributary spawning Flannelmouth Sucker.