Abundance estimates can be crucial for managing species of economic concern. The accuracy of these estimates can depend on the methods used to track animals and to estimate abundance from tracking data. We tested experimentally if disparate estimates of trapping efficiency calculated for sea lamprey (Petromyzon marinus) in the St. Marys River near Sault Ste. Marie, Canada could be explained by effects related to the invasiveness and handling involved in tagging or the tag size used in the marking procedures. Trapping is used to gauge adult abundance, trapping efficiency, and success of a binational sea lamprey control program in the Laurentian Great Lakes, North America. Our experiment compared nightly catches of sea lamprey marked with external fin clips, surgically-implanted passive integrated transponder tags (PIT-only), and surgically-implanted PIT and acoustic tags (PIT+acoustic). We found no evidence that the probability of being trapped was affected by the added invasiveness and handling of internal tagging. Nightly recaptures of PIT-only tagged sea lamprey, relative to fin-clipped sea lamprey, were not different from expectations based on the numbers of individuals released from each treatment group. Conversely, there was evidence of effects related to tag size. Nightly recaptures of PIT+acoustic tagged sea lamprey, relative to PIT-only tagged sea lamprey, were lower than expected based on numbers of individuals released from each treatment group. Effects related to tag size partially explain the disparate estimates in trapping efficiency observed for sea lamprey.