<p>The aim of this study was to explore the freshness indices of sea urchins. Uncracked sea urchins and their gonads were stored at low temperatures, and changes in the contents of adenosine triphosphate (ATP)-related compounds [ATP, adenosine diphosphate (ADP), adenosine monophosphate (AMP), inosinic acid (IMP), inosine (HxR), and hypoxanthine (Hx)] and in various freshness indices in the gonads were investigated. In the uncracked urchin storage tests using the sea urchins <i>Mesocentrotus nudus</i> and <i>Pseudocentrotus depressus</i>, the content of ATP-related compounds did not change significantly until death; however, the ATP percentage (ATP%) and adenylate energy charge (AEC) decreased in sea urchins with reduced vitality, suggesting that these are useful indicators of vitality in live urchins. In the gonad storage tests using these same two sea urchin species and the sea urchin <i>Diadema setosum</i>, during the storage period ATP decreased, and HxR and Hx increased, whereas ATP% and AEC decreased. In <i>M. nudus</i> and <i>D. setosum</i>, the<i> K</i> value (ratio of the amounts of HxR and Hx to the total amount of ATP-related compounds),<i> K′</i> value (ratio of the amount of IMP, HxR, and Hx to the total amount of ATP-related compounds), and Hx/AMP ratio increased after 12 days of storage. These results suggest that ATP% and AEC are valid indicators of gonad freshness, whereas the <i>K</i> value, <i>K'</i> value, and Hx/AMP ratio are indicators of early putrefaction.</p>