Abstract Sea urchin Tripneustes gratilla is one of an economic important fisheries resources product for localities at Wakatobi archipelago. High demands for sea urchin gonad have intensified high fishing activity. We hypothesize that sea urchins at Wakatobi have overfished. To answer that hypothesizes; we measure the density and its test diameter size at two different sites. They are Pulau Tomia (inhabited area) and Pulau Sawa (uninhabited area and very distant from the localities). The results show that sea urchin density and its test diameter is significantly different. The densities (mean ± SE) Tripneustes gratilla at Pulau Sawa and Pulau Tomia are 10 ± 0.6 (ind./m 2 ) and 2.7 ± 0.9 ind./m 2 , respectively. Moreover, the test diameter at Pulau Sawa and Pulau Tomia are 69.7 ± 2.1 mm (mean ± SE), and 58.5 ± 1.7 mm (mean ± SE), respectively. These results have indeed shown that overfishing has occurred. Therefore, sea urchin with test diameter 66–75 mm, 76–85 mm, and 86–95 mm have disappeared at Pulau Tomia. Our conclusion reveals that fishing of sea urchin Tripneustes gratilla at Pulau Tomia has overfished.