Covert mortality nodavirus (CMNV), a unique aquatic pathogen first isolated from shrimp, has a broad host range that includes crustaceans and teleosts. The sea cucumber Apostichopus japonicus, an Echinoderm, was recently shown to be a host for CMNV. To investigate the histopathology of CMNV infection in sea cucumber, four out of 61 A. japonicus individuals that tested positive in reverse transcription nested PCR (RT-nPCR) assays were furtherly analyzed through in situ hybridization (ISH), histology, and transmission electron microscopy (TEM). Extensive bluish-purple positive hybridization signals of CMNV probe were found in tissues of the respiratory trees, intestine, and gonad in conjunction with a variety of pathological lesions, including vacuolation, karyopyknosis, and muscle necrosis. Also, masses of CMNV-like particles were observed through TEM in these tissues, as well as in the body wall and longitudinal muscle. Sea cucumber is important in Chinese aquaculture, and CMNV infection of gonad tissue indicates a potential for vertical transmission that could negatively impact larval rearing.