Managers frequently rely on conservation hatcheries to maintain declining fish populations in the wild, which is the case for bonytail Gila elegans, an endangered species endemic to the Colorado River basin, USA. We used a multi-agency database of stocking, capture, and PIT-tag detections during 2013-2021 across the upper Colorado River basin to assess if re-encounter probability of bonytail varied among seasons, stocking habitats (mainstem, tributary, and off-channel), and with length-at-stocking. Because of previous observations of recaptured bonytail in poor body condition, we tested for differences in condition among stocking habitats. Of 325054 stocked bonytail examined, 90% were never re-encountered. Most re-encounters (93%) were PIT-tag detections near stocking locations. Re-encounter probability was low regardless of stocking habitat, and 95% of fish were at large for <195 d. The effect of length-at-stocking on re-encounter probability varied among habitats and was positive in mainstem and tributary and negative in off-channel habitats. Slopes of length-weight relationships of recaptured fish differed among stocking habitats. Given consistently low re-encounters of stocked bonytail in all habitats regardless of length-at-stocking or stocking season, we recommend managers consider refining the stocking program to better identify specific factors that affect survival, including stocking fish into intensively managed off-channel habitats which afford greater control of abiotic and biotic conditions than riverine habitats. If stocking continues among multiple habitat types, at a minimum we suggest stocking fish at consistent locations over time to better allow for quantitative assessment and to ensure fish are stocked into water temperatures that align with optimums for growth, recovery-from-handling, and survival.
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