Wild animal welfare is increasingly recognized as a critical component of scientific research. It is best understood at the individual level and defined by the quality of an animal’s subjective experiences. Individual identification is a cornerstone of wildlife studies, crucial for tracking life history and informing management decisions. There are a variety of techniques available that give an individual unique identification, but little is known about the stress impacts that the techniques directly or indirectly cause. Glucocorticoids, such as corticosterone (CORT), play a key role in the vertebrate stress response and are commonly used as biomarkers to assess stress, disease, or environmental challenges. This study focuses on Siren intermedia, an understudied, fully aquatic salamander species with characteristics suitable for water-borne hormone collection. By comparing CORT levels in response to a common identification technique (PIT tagging) and a non-invasive alternative (image recognition), in a field setting, we aim to gain insight into wild animal welfare. We obtained 3 CORT samples (baseline, agitation and recovery release rate) from each siren at initial capture and one following recapture to analyze the magnitude of stress response (MSR) and negative feedback (NF). Temperature and capture history were the strongest predictors of MSR with new captures showing elevated MSR, as temperatures increased. Technique showed marginal effects on MSR and may require more data to clarify its role. For NF, baseline release rates and capture history were the main drivers. Our study demonstrates that both identification techniques trigger measurable physiological stress in sirens. Choosing the most suitable identification technique is complex and requires thoughtful consideration of numerous factors. Although we cannot definitively determine that one method is significantly better for animal welfare—given the nuances involved—our findings offer valuable insight to help researchers assess the welfare of wild animals.