The microsporidium Glugea stephani is endemic in winter flounder from the New york – New Jersey area. The prevalence of infection fluctuates with water temperature on a seasonal basis, increasing in summer and decreasing in winter. From March 1981 through December 1983, 32 monthly collections were conducted. During this period 4002 winter flounder were caught and examined, 301 (7.5%) of which were infected. Data collected during the study indicated that although several factors may influence the host–parasite interaction, only water temperature changes could be statistically correlated with G. stephani infection in this winter flounder population. In an effort to determine what factors other than temperature affect prevalence of infection, fish length, sex, diet, and spawning behaviour were examined. Although these factors do not, at first, appear to influence infectivity, stress imposed on the host by physiological and environmental changes may be significant. Our results are compared with those from G. stephani in its type host, the European flounder Platichthys flesus.