In situ ecological studies on obligate cave-dwelling aquatic animals are scarce at best. This is particularly true for capture-mark-recapture (CMR) studies that form the basis of understanding population structure and dynamics. Here, we report on the in situ underwater application of the Visible Implant Elastomer (VIE) tagging system on the olm, Proteus anguinus, an obligate cave-dwelling aquatic amphibian. We tagged seven adult individuals and monitored the population during 31 dive transects during four years. We found that VIE tagging is applicable underwater. Based on our recaptures, the tags were recognisable after four years and the recaptured three individuals exhibited extreme site-fidelity. Our results indicate that CMR studies are feasible in underwater cave ecosystems without even temporarily removing individuals. In situ underwater tagging also holds great potential for studies of other aquatic ecosystems, where removing animals from water, their habitat or territory is problematic for ethical, logistic or scientific reasons.