Populations of sea cucumbers, including the Japanese common sea cucumber Apostichopus japonicus, have been seriously depleted worldwide due to overfishing. Mark-recapture study is an efficient means of collecting ecological data. However, the use of such a method in sea cucumbers is difficult because they lack hard tissues in the body wall. Here we tested the viability of various tagging methods on A. japonicus. First, we applied conventional tags using four different methods [single spaghetti (T-bar) tagging, double spaghetti tagging, ribbon tagging, and Atkins tagging] to ten individuals per method in aquaria for 14 days. Of the methods used, single spaghetti tagging had the highest retention rate. Then we examined the retention rate of single spaghetti tags on ten individual sea cucumbers for up to approximately 6 months in rearing conditions. The single spaghetti tagging method showed a retention rate of 100% over at least 7 days, and 50% of the tags remained embedded after 56 days. The longest duration of tag retention was 174 days, at which time the experiment was terminated. These results indicate that single spaghetti tagging is reliable for both short- and longer-term studies, making it a useful tool for ecological and conservation studies in sea cucumbers.