The living environment in spacecrafts would be progressively contaminated by microorganisms. Various microorganisms have been isolated from on board manned spacecrafts and they have been brought with commodities, crew members themselves, and so on. So it is unavoidable to bring microorganisms such as fungi and bacteria into manned spacecrafts. Some microorganisms are known as possible allergens in our living environment and many researchers are studying the correlation between environmental microbiota and allergic reactions. Normal flora is thought to be strongly affected by living environment. So we should monitor and evaluate both of environmental microbiota on board spacecrafts and normal flora of crew members, and finally develop effective medical countermeasures to protect crew members against microorganisms in manned spacecrafts, which have confined living space under microgravity.