The purpose of this study was to clarify which oral environmental factors affected number of microbes in saliva in an edentulous environment. We enrolled 68 edentulous subjects in the study. Numbers of total anaerobic bacteria and Candida species in saliva were determined. Age, sex, un-stimulated salivary flow rate, pH and viscosity of saliva, histatin level in saliva, tongue coating status, tongue pressure, denture plaque status, material of denture base, duration of edentulism, frequency of self oral health care and number of cigarettes per day were also investigated as oral environmental factors. Correlation between number of total anaerobic bacteria or Candida species and each oral environmental factor was determined with the Spearman rank correlation coefficient. Stepwise logistic regression analysis was used to identify which factors were significantly associated with level of total anaerobic bacteria and Candida species. Correlation and stepwise logistic regression analyses revealed associations between un-stimulated salivary flow rate, tongue coating status, denture plaque status or frequency of self oral health care and number of total anaerobic bacteria. The correlation analysis showed a significant correlation between age and number of total anaerobic bacteria. Stepwise logistic analysis revealed associations between pH of saliva or viscosity of saliva and level of anaerobic bacteria; it also revealed associations between histatin level in saliva or un-stimulated salivary flow rate and level of Candida species. We conclude that salivary flow rate, in particular, affects number of salivary microbes in an edentulous environment.