F/V Shinsei Maru No.3 has been engaged in Exploratory Fisheries since 2003. Furthermore the vessel has conducted research activities under CM24-01 in division 58.4.4 since 2008 and provided significant scientific information on toothfish. For the rational utilization of toothfish resources in data-poor areas, we understand that tag-recapture research plays a central role for the stock assessment so we have exerted as much efforts as possible to complete our research plan. However, in course of conducting our research, we experienced operational difficulties that could diminish the effectiveness of the tag-recapture program. These operational difficulties arose from the mismatching between the current Conservation Measures and regulations on Exploratory Fishery, and the actual on-site condition that limits the fishing practice at sea such as: toothfish distribution; fishing ground topography; and sea condition. In this paper, we introduce such operational difficulties in conducting toothfish research in data-poor areas to facilitate understanding of actual fishing operation and to stimulate discussion for practical improvement of the research.