Abstract： Objective To investigate the prevalence and related factors of recurrent aphthous ulcer (RAU) in the naval shipboard personnel. Methods Cluster sampling was carried out with each naval vessel as a sampling unit. A questionnaire was implemented to survey the incidence, therapy and results of RAU among the naval shipboard personnel, then, statistical analysis of the results was made. Results The prevalence rate of RAU reached 29.8% in the investigated population, of which the prevalence rate of the surface ship personnel was 28.5% and that of the submariners was as high as 36.1%. Significant differences could be seen between them (P<0.05). The survey of prevalence rate of RAU through independent investigation revealed that differences could also be seen in officers and men with different service years. At the same time, most patients were affected to some degree psychologically and in their daily work. Conclusions The prevalence of RAU was higher among the naval shipboard personnel. Measures should be taken to prevent and treat RAU that occurred among the naval shipboard personnel.