Several tagging methods have been tested to assess important aspects on ecology, such as population dynamic, movement pattern, and behavioral studies. The use of external and internal tags has been extensively used for individual identification in sea urchins. Different types of tags have been used in Echinometra lucunter, considered the most common sea urchin in the Caribbean. We evaluated whether PIT-tags and S-tags may affect retention, survival and growth rates under laboratory conditions, using the sea urchin E. lucunter as a model. The type of tag was critical in terms of retention rates, with significant differences between PIT-tag and S-tags groups (Kruskal–Wallis, H = 5.33, p = 0.021), and mortality exhibited similar rates among treatments. No significant association was detected between initial maximum test diameter and the number of weeks the individuals retained neither the PIT-tag (r = −0.09, p = 0.620), nor the S-tag (r = −0.175, p = 0.413), and no significant differences in growth rate were detected among treatments (F = 1.66, df = 2, p = 0.401). We do not recommend the use of S-tag due to low retention; but we support the use of PIT-tags in E. lucunter for their positive performance displayed in terms of retention and survival but with caution, particularly in those studies requiring 80% or higher retention.