Since small mammals from seaports have relative higher seroprevalences of hantavirus, this seroepidemiologic study was conducted on the isles in Kinmen and Lienchiang Counties along the coast of southern mainland China to determine whether seaport may play the role as a source of hantavirus. Among six species of small mammals trapped in Kinmen County, only male Mus musculus (6.7%) and Rattus losea (5.3%) were found to be positive. In Lienchiang County, five species of small mammals were trapped and positive findings were obtained only in male R. norvegicus (9.3%), male M. musculus (7.7%), and female R. losea (1.6%). There was no significant difference in the seroprevalence between the two counties (Kinmen 3.8% vs. Lienchiang 3.9%). The positive rate in Liaolo (17.9%) of Kinmen County was significantly higher than the remaining trapping stations and those in Matsu Distillery (10.3%) and Fushing (5.8%) of Lienchiang County were significantly higher than the remaining ones. Moreover, a significant inverse correlation was found between the seropositive rate and the distance of small mammal sampling sites to the seaport (p < 0.01). These findings suggest the role of seaport as a source of hantavirus.