From May to June in 2006, an epidemic disease named stomach atrophy syndrome in sea cucumber Apostichopus japonicus occurred widely in Liaoning area during the hatching period. The influence area was large and mortality was high and no efficient remedy to control the development and spread of this epidemic. T his epidemic occurred mainly at 5 to 7th days after larvae hatching. With the increasing of spawn times, the infected time became ahead and the larvae were diseased after being hatched 1 to 2 days. The stomach of diseased larvae shrinked gradually and the stomach wall tended to thick, rough and distorted till the stomach became nearly small globosity. In order to understand the kinds of pathogeny, the A. japonicus larvae and their parents were detected by the observations of negative stained samples and ultrathin sections. The tissue homogenate was prepared from the A. japonicus larvae and the tissue of their parents. The tissue samples were centrifuged (13 000 r·min-1, 8 min) twice after homogenizing, freezing and thawing. The supernatant solution wa s dripped on to a copper net and stained with 2% PTA for 5min and observed with electron microscopy. The diseased animals were also fixed in 2.5% glutaraldehyde and 1% osmium tetroxide solution. Samples were dehydrated and transferred into Epon 812 resin and then cut. Sections were stained with lead citrate and uranyl acetate and observed. The observed results showed that amount of virus particles were observed on negative staining samples in the larvae homogenate, and most of them are approximately 75-200 nm in diameter. The virus particles were also found in the gonad, body wall, the alimentary canal and the respiratory trees of corresponding parents hatched the larvae. Farther examination of larvae by electron microscopic observation of ultrathin sections showed that the virus affected mainly the connective tissue cells and epithelial cells. The virions were approximately spherical or hexagonal with envelope, and the core structures with high electron densities in the envelope were observed. The gonad, the body wall, the intestines and the respiratory tree of paternal and maternal parents were also observed by negative staining. The results showed that this kind of virion located in all the tested organs and tissues.