In Japan, seed production techniques have been developed for about 80 species of marine fish and shellfish. However, mass mortalities due to infectious and non-infectious diseases have often occurred in larvae and juveniles reared in hatcheries. Among these problems the viral and bacterial diseases are reviewed in this paper. Since around the middle of 1980's some new viral diseases such as viral epidermal hyperplasia (herpesvirus infection) in the Japanese flounder, viral ascites (birnavirus) in yellowtail, viral nervous necrosis (VNN) (nodavirus) in striped jack and some other fishes, and baculoviral mid-gut gland necrosis (BMN) in kuruma prawn have been reported. It was demonstrated that the selection of virus-free spawners based on the diagnosis by polymerase chain reaction (PCR) could serve as a control measure against vertical transmission of the pathogen in striped jack. Vibriosis, pasteurellosis, gliding bacterial infection and other bacterial diseases have occurred in various marine fishes during their juvenile stages. On the other hand, larval fish most frequently develop intestinal infections represented by bacterial enteritis with Vibrio sp. INFL in the Japanese flounder. Live foods contaminated with pathogenic bacteria have been suspected to serve as an important source of these intestinal infections.